After the last map issue, I decided to run through multiple civs to see if everything's been dealt with. Unfortunately, there are still a couple of issues with squares that should be Historical being marked as Foreign. Here's all that I could find:
England - the Rockies (1E of the Coal), the southern tip of Sri Lanka, and the Coal on the east coast of Australia
Spain - most of the Rockies within Mexico's flip zone
Rome/HRE/Turkey/Prussia: 1N of Belgrade (though Rome is probably the only one who cares)
Persia/Arabia/Turkey/Iran: 1W of Tebriz (though this spot is pretty bad, so you might want to leave this Foreign just to discourage the AI)
France: Eastern Tasmania (though given that France probably shouldn't have any Historical territory in Australia/Tasmania/New Zealand in the first place, this can probably be ignored).
There are a couple other isolated spots, but they are typically all areas that are either irrelevant (in the middle of desert/tundra) or are overshadowed by other, more important cities (a solitary square in Anatolia that's part of both Constantinople's and Konya's BFC, for example). If I find more, I'll let you know.