Since Livingston was kind enough to label commonly missed spots, I thought I'd go through them and point out how to reach them. Most of these are going to be simple, straightforward directions like "SW corner of Zone X" meaning "check southwest corner of zone X," but some spots are trickier than others and will receive more attention.
If you'd like specific directions to a particular spot or want your map compared to make sure you've cleared as much as you could have, please head on over to the 100% Canthan Cartography discussion thread and post there. Even if I can't answer you, someone definitely will
Shing Jea Island
1. North wall of Minister Cho's Estate explorable. Check the beach on both sides of the rock outcropping.
2. NW corner of Minister Cho's Estate explorable.
3-6. West wall of Kinya Province. Make sure to go as far west as you can on all islands and beaches.
7. SW corner of Panjiang Peninsula. Check from east (dock) and north (beach).
8. Middle of Panjiang Peninsula. Walk the edges of the bay.
9-10. The "mountain spot" west of Tsumei Village. This spot cannot be cleared completely, but 9 can be reached from SE corner of Kinya Province and 10 from NE corner of Panjiang Peninsula. Go as far NW as you can when exiting Tsumei Village to clear 10.
11. East wall of Panjiang Peninsula.
12. Shing Jea Arena. The battle area of this arena is open to characters level 10 and under. The staging area of this arena is open to all characters. Talk to the arena guard in Shing Jea Monastery to enter.
13. SW corner of Shing Jea Monastery outpost, behind the Xunlai Agents.
14. For Tyrian characters who never entered Monastery Overlook, parts of that zone can be cleared from Saoshang Trail and the docks of Seitung Harbor.
15. The docks of Seitung Harbor. Make sure to go as far south as you can.
16. SW corner of Zen Daijun explorable. Gates leading to this area are closed in the mission.
17. The south wall of Zen Daijun explorable. This area may be open for exploration in the mission but the north path is much easier for mission completion.
18. SE corner of Zen Daijun explorable. Gates leading to this area are closed in the mission.
19. SE corner of Haiju Lagoon. Make sure to check behind the resurrection shrine.
20. East wall of Haiju Lagoon. Clear from the "Sentimental Treasures" quest island north of the spot. Beware of the Ritualist boss.
21. Hanzing Pier, endpoint for "Captured Son" quest. Go as far east as possible.
22-23. North wall of Haiju Lagoon. Go as far into the water as possible.
24. North wall of Jaya Bluffs. Instead of just exploring it from Zuuyun Point (where the road below goes into the mountain), walk the cliffs to the east and west.
25. Sizhou Hall, endpoint for "Looking for Trouble" primary quest.
Kaineng City
1. West wall of Wajjun Bazaar. Head NW from Nahpui Quarter. Easiest if "Seek Out Brother Tosai" quest from Kaineng Center is active, as it turns all regular Am Fah spawns in Wajjun Bazaar into NPCs rather than enemies.
2-3. Make sure to hug the edges of the island as closely as possible - you can uncover some spots in the water that show as a "vertical line" glitch on the world map the way west edge of Dunes of Despair mission in Tyria does. The "U" map and zoomed-in overview map don't show this line.
4. West wall of Kaineng Center outpost. Go SW past the armor crafters or NW past the Canthan Ambassador to reach the docks.
5-6. NW and NE corners of Bejunkan Pier. Check the edges of both levels (up the stairs and down at the docks).
7-9. North wall of Raisu Palace explorable. To clear 8, walk the piers.
10. NE corner of Imperial Sanctum mission, accessible only from Shiro's banishment path. Hug the cliff as closely as possible. If this spot does not clear immediately, walk back along the edge from the first spirit to the east side of the banishment area. For tips on getting banished, see this thread.
11. SW corner of Imperial Sanctum mission, accessible only from the battle area. Shiro always banishes players to the same path. To uncover the rest of the area, walk the edges of the battle area without engaging Shiro.
12. Tahnnakai Temple explorable. This area cannot be reached during the mission due to locked gates. In the explorable, make sure to walk both the east and the west side, as they form separate paths and do not link up.
13. South wall of Dragon's Throat outpost. Dragon's Throat is bugged in that you cannot clear any fog from inside the outpost and the PC marker does not show up on the overview map (the same way it does not show up inside Dragon's Throat mission). To clear this, walk out into Shadow's Passage and get as close to the portal without zoning back in as possible.
14-15. East and south walls of Vizunah Square mission.
16. North wall of Shenzun Tunnels. Start from Tahnnakai Temple and go west; you'll only need to fight/run past one mob of Am Fah.
17. SE corner of Undercity. This is one of the spots where Xaquang Skyway does not coincide with Undercity, so this spot must be cleared from below.
18. Center of Shenzun Tunnels. Many people miss this spot when following the "To Tahnnakai Temple" quest.
19. NW corner of Sunjiang District explorable. Parts of this spot may be cleared from east wall of Shenzun Tunnels.
20. This spot can be cleared from inside Zin Ku Corridor outpost. Hug the corner directly NE of the spot.
21. SE corner of Tahnnakai Temple explorable. A lot of people miss it when rushing to Vizu during the mission. A related spot further south is the east wall of Zin Ku Corridor, behind the weaponsmith.
22. East wall of Sunjiang District explorable.
"Middle Cantha"
1. SE corner of Nahpui Quarter mission and SW corner of Nahpui Quarter explorable. You cannot clear this spot completely but can hug the edges closely, especially since a lot of people don't clear all they can in the burned-out home of Am Fah (south wall of Nahpui Quarter explorable).
2. South wall of Shenzun Tunnels. Most easily reached by starting in Senji's Corner and going through Nahpui Quarter explorable.
3. NW corner of Pongmei Valley.
4. The "farmland spot" east of Maatu Keep. The best way to clear this spot is to hit SW corner of Sunjiang District explorable, but you may need to hug the walls in all surrounding areas - SE corner of Shenzun Tunnels, east wall of Maatu Keep and north wall in Pongmei Valley - as well. Sunjiang District mission won't let you reach the SW corner of the zone as the area is closed off by a gate.
5. East wall of Pongmei Valley and north wall of Boreas Seabed outpost. To get the north wall of Boreas Seabed outpost, use the bridge behind the Xunlai Agent.
6. North wall of Boreas Seabed explorable.
7. North wall of Mount Qinkai.
8-9. South wall of Pongmei Valley.
10. West wall of Mount Qinkai.
11. NW corner of Arborstone explorable.
12. West wall of Arborstone explorable.
13. SE corner of Arborstone explorable or NW corner of Ferndale, depending on which side of this spot you're missing.
14. North wall of Ferndale.
15. West wall of Kurzick Aspenwood Gate outpost.
16. This spot is cleared by asking the Luxon Commander in Luxon Fort Aspenwood outpost to Replay the mission cinematic.
17. NW corner of Jade Quarry
battle area. To clear this spot, check behind the guardpost NE of the yellow quarry. Make sure to hug the walls inside the yellow quarry as well.
18. East wall of Jade Quarry battle area. Check the east wall of the Luxon starting area, behind the guardpost north of the green quarry, and inside the green quarry.
19. SW corner of Jade Quarry battle area. Check the west wall of the Kurzick starting area and behind the guardpost SW of the yellow quarry.
20. East wall of Ferndale.
Echovald Forest
1. East wall of Melandru's Hope.
2. NW corner of Melandru's Hope.
3. SW corner of Saint Anjeka's Shrine outpost, behind the henchmen.
4. SW corner of Drazach Thicket.
5. NW corner of Eternal Grove explorable.
6. SW corner of Mourning Veil Falls.
7. SW corner of Amatz Basin mission.
8. South wall of Mourning Veil Falls.
9-10. North wall of Morostav Trail.
11-12. NW corner of Unwaking Waters explorable.
13. NW corner of Luxon Unwaking Waters outpost or NE corner of Unwaking Waters explorable.
14. East wall of Silent Surf and south wall of Seafarer's Rest outpost.
15. South wall of Silent Surf, on the island.
16. East wall of Unwaking Waters explorable.
17. South wall of Unwaking Waters mission. Head south after coming out of the gate, but remember to help the other team finish the mission if they're not all henchmen to avoid giving cartographers a bad name 
18-19. East wall of Morostav Trail.
Jade Sea
1. NW corner of Eredon Terrace outpost.
2. North wall of Maishang Hills.
3. South wall of Maishang Hills, SW corner of Maishang Hills (hug the wall facing east), and NE corner of Archipelagos.
4. SW corner of Maishang Hills (hug the wall facing west).
5. Zos Shivros Channel mission.
6. SE corner of Archipelagos.
7-9. West wall of Gyala Hatchery explorable. Sometimes the island above 7 also isn't completely cleared; check the west wall of the gated quarry next to it.
10. There is supposed to be a tiny island north of the Leviathan at this spot. To clear it, head west out of Leviathan Pits, kill the boss mob and the oni spawn on the big island, and squeeze into the southern corner of the big island as tightly as you can. Move around and change the direction you're facing to make sure you clear the spot.
11. NE corner of Silent Surf and west wall of Rhea's Crater.
12. SW corner of Aurios Mines mission.
13. NE corner of Aurios Mines mission.
14-15. North wall of Rhea's Crater. 14 is rather easy to clear, but 15 pops up only when heading east in the north hallway, up against a block of jade that juts out of the wall. Clearing the boss spawn west of 15 might help as well.
16. NE corner of Gyala Hatchery explorable.
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