False Emperor has a couple still, on the final fight for instance:
The Boss will often be in a different position to where he looks visually, IE he looks like he is standing next to the healer but he is really next to the tank.
Players can get knocked into various parts of the ship so they can move for about 30 secs.
These can all be avoided through positioning etc. However, they are still bugs. And thats not counting the Jindo Krey bugs mentioned above (which I havent seen personally). Also we have had it so that up to two people in the party dont see the ship at all.
Most of the bugs in HM FPs have workarounds either in composition, positioning, movement etc. Personally, its the composition type that I would like to see have a higher priority