Here is a list of "bugs" I encountered while playing MoO2, although none of them prevent me from playing the game.
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When prompted to enter a name, say for a planet, the game will become unresponsive. Both mouse and keyboard will seem to stop responding, but by repeatedly pressing Enter or moving the mouse and clicking the continue button, you can get past the prompt.
What seems to happen, is that the game will freeze for a period of time, then quickly respond, then freeze again. Right before the game responds, it will begin to record any mouse and keyboard prompts: this means that even if you wildly move the mouse around, only half a second of mouse movement is recorded and then shown. This does make colonizing planets a bit tedious. -
When text flashes or is highlighted, the game seems to slow down, a lot. This occurs when selecting things to build on your planet, choosing research, and especially when custom building your ships. I'm not sure if its a Direct X 2 issue (installed it with game, is included on cd) or a crossover issue.
Everything else seems to be stable. I have yet to see if the Plasma Cannon / Gauss Cannon will shutdown the game like they did on Windows XP when I custom built my ships. If I find more issues I'll post them here.