Some wonky behavior in The Last Hurrah due to the way the mission is designed. Nothing that makes the mission unplayable, but enough to get your attention.
1) You can't really issue precise orders to your wingmen for most of the mission because you can't target specific enemies. However, if left to their own devices, your wingmen will do stupid things like attack the Archon (even though they can't damage it) while ignoring other, better targets. This may be partly related to the loadout you choose (I seem to recall having more well-behaved wingmen depending on what their secondaries were), but I'm not sure.
2) It looks like certain ships can't be destroyed until they become visible on sensors. This is certainly the case with the Archon, but it also leads to other silliness; there's at least one Azrael transport that cannot be killed until the EMP burst sufficiently wears off, meaning your wingmen will shower it with fire to no effect. I believe this is also true of one of the cruisers.