Well at this point, one of the handicaps to mods getting bugs fixed is that I notice a lot of them seem to work around bugs rather than actually try and get them fixed. As a result you have various features that don't work, but nobody actually knows because nobody bothers to report them. 
Before Redmenace starting providing builds we also had the problem of being several months behind in builds and so there was no point putting stuff on mantis when your running way outdated builds (when the problems were fixed when we got a new build)
Well the only one we have a full work around for is the colliding support ship problem which Goober thought was quite funny.
He suggested a work around for the play dead problem by disabling all the 'dead' fighters. However they then self destruct after a certain amount of time as the game does that to disabled ships in wings to allow additional waves to arrive. However 20 fighters exploding together for no reason kind of spoiled the mission so I left it as it is. That particular error seems to be very random.
The protect flag bug can only be bypassed by ordering all wings to ingore the protected target, since the capships also follow the order it's an effective workaround, but annoying to remember to do.
This crashing problem only I can confirm, I get a CTD on mission load and a 'DAMAGE' error in the debug builds (though not in the latest cvs build I tried today) Last build I have that this doesn't happen with my last own CVS build in September. I'm trying to narrow it down with the little time I have for testing.