I've also experienced this issue before.  I'm afraid I don't have any solutions for you.  I do know that you won't run into any problems if you're just changing the difficulty of the AI, but if you actually put an AI in the position formerly held by a human player it bugs up.

Anyways, a good way to actually watch the game unfold is replays (they're automatically generated) and you can watch what the AI is doing as it's doing it.  Just a word of warning; watching the AI is a great way to learn the basics, but anything more subtle or complex really isn't its forte to begin with.  There are some great replays of actual players demonstrating good early-game colonization pace and fleet management.