thx Mace,
in all the "Masters" missions the ships from allied races are still technically your allies, but you can target them and they'll turn on you if you damage them (any AI will turn on each other if they happen to damage each other accidentally, e.g. with t-bombs or esgs)
I haven't seen a CTD yet, but I've been doing most of the testing on the EAW side. If your ship was undamaged at the start of the mission then something funky is definitely going on.
EDIT: Was it using the stock shiplist, OP+ v2.0, OP+ v2.1, or OP+ v2.1b? (just in case it's related to a shiplist issue)
dave