Amusing: if you conquer an opponents colony whilst that colony is taken over by that opponent's Mother Country, you capture not only that colony but also its contents: leaders, armies, explorers, settlers — the whole deal! I suspect the program recognises only one Mother Country regardless of the number of nations involved, so the capture is interpreted as you regaining control over your own colony.

Less amusing: sometimes some of my colonies' populations keeps dropping / fails to grow, even though there is enough food, housing, work to be done and a few level 4 churches boosting immigration. I haven't found out what causes this yet, but I suspect it has something to do with having a lot of gold mines. Perhaps my miners are running away with MY gold!

I found a way to get settlers even if you don't have the resources to build one. You can build settlers from all of your houses at once. Is it even possible to fix this game at this point? Maybe a community created unofficial patch to fix some of this stuff? Was source ever released?

It seems by around turn 110 or so I start getting units that will not respond to movement orders. To get around this, I have found that ordering it to explore (whether or not there is territory to explore) will "unstick" the unit.

I think I know how exactly this happens, as I see that on my ships a lot.

If you attack one target (ship) with multiple units (ships), and one of first attackers destroy it already, all others left with that order start next turn grayed out and with no movement, and next turn have movement restored, but must be "unstuck" with Explore command.

Never seen anything like this for ground units, but it may be possible too.

Have heard a rumor High Native can exploit this - if there a colony currently under rule by Mother Country, High Native can "recapture" it as well, and from here, basically become European player. Rarely play High Native, not managed to do this myself so this really is more of a gossip. But sounds possible. Do you have any goods output? My best guess is, you don't have enough food. Check the "population detail", if there a "Colony is starving !" warning it is it. Your stored crops is first eaten, then used for goods making, and only then harvested. Only amount you can eat is subtracted from planned income in colony overview (and you can't eat more than is stored), so it rarely if ever drop negative because of starvation. You need at least one crops for every hundred of population (rounded up, 1001 people need 11 crops) in storage at end of the turn.
A good rule of thumb I try to follow is to have in storage at least twice the amount of crops you consume per turn. This gives you some space to maneuver in.

Some more Quirks:

- If your colony center falls in "hostile territory" due to nearby native village (this may happen in multiple ways: you can build there right away, a formerly friendly tribe can get angry on you, villages may grow - especially after discovered by federating High Native, even get federated - and then your relations with High Native player comes in play) you can't enter your colony by just moving a unit over colony center, it will just step on it.
Workaround is to use "Unit List" (from top menu) to manually place it in that colony then. Must stay over left corner of colony center, from eight squares adjacent to that corner it may or may not work.

- If you manage to build more than 100 buildings in single colony (not impossible at all, although not usual as well) the "Building List" button will crash the game. Looks like someone got stingy with limit on that list... anything else seems to function as normal. 100 is not a number you could easily estimate, but since game auto-saves, you at worst lose one turn worth of work upon discovery you breached this limit (well, sometimes one turn may as well be worth an hour if not more...); after that, just remember you can't use "Building List" in that particular colony anymore.

- If you order your unit to move exactly to a special discovery square, it will head away in what looks like random direction. For example, once one of my leaders stubbornly climbed up a mountain when ordered to go guard a wheat field. No idea where it would end up in a long run...
To work around this, order it to go to place right over the desired target, then catch and stop him right there.
(now, would only dream there was a "sentry" command to not pollute "next" button with intentionally stationary units...)

- You can manage single-turn delay shipments over any distance. Need desired amount in storage at destination, so this is more for smooth strategic play not really a day-saver bug: 1) create a transfer as usual; 2) go to the destination and make changes to that transfer from here. It now will register as single-turn transfer, until you re-open it from the source again.

- If you have no units at all in a colony, but some non-attached military units on the overland map, those may come to defend the empty colony - not sure does distance matter here, if so it is huge, possibly this is a bug and they may be anywhere. Also not sure can those overland units be lost this way or those are virtual copies that defend in this case (only have seen this event twice, both times got raided but won the fight with no loses).

- If game exits to main menu when you try to create new custom game or mapped scenario, the possible cause is, you have too many saved games / mapped scenarios in games directory. And the number required is not large at all, for me, it is enough to have 28 saved games / scenarios to start experience problems. If you have really many, the saved games list itself can get messy (not that it wasn't already, but even more). You can try to delete some from that in-game menu, but that may or may not work, for me, it sometimes remove them from list, but not wipe the files... but number of files is what likely counts.
So, the solution is to manually delete or move the saved game files. I like to create and keep around a lot of unnecessarily saves, so I move all saves of each long game to its own sub-directory when I want something new, and back when I want it again after a while. The save game files is those with 8 hex-digit names *.TE2 *.GE2 extensions.
The oldest two of those pairs correspond to tutorials or something... not a great loss, if you accidentally mess with those, but still, be aware.