1) Yes - click on govern on the bottom right of screen, then enchantments tab, and you can remove enchantments there. It's not possible from the individual city interface.
Actually, on the city detail screen, in the upper left hand corner, there are icons for the enchantments. On top of each icon is an 'x'. If you click it, the enchantment can be dispelled. Much easier than hunting them down in the ledger.
2) The colored lines around my borders for cities/outposts randomly vanished in the game I'm in at the moment.
Happens when you reload too many times. It's a memory leak the developers have not hunted down yet. Restart the game.
3) Is it a bug or intentional feature that I can't seem to place piers/logging camps on river/tree tiles
It's a goddamned feature. I hate it too, but it's here to stay. It used to be the sensible way around, but it was decided that careful laying out of your city should NOT work out to your advantage, so now if your city does not start next to a forest, you'll never build a logging camp.