Ok here's an obvious bug that I am surprised that nobody has noticed. See feature adjustment #34 which is 'Nero 2 Timer'. Nero 2 doesn't have a timer! Or is it supposed to and it doesn't use one? This appears directly related to the inserts going into a fast flicker after a certain period of time. The mission itself isn't running off a timer, but the insert blink rate seems to be. I verified this by setting the timer to 10 and the inserts start to go crazy after about 10 - 15 seconds. Therefore I recommend setting Nero 2 timer to 60 so the inserts don't screw up for as long as possible. I bet this was also related to Nero 2 shots disappearing and not coming back..
There may be other timer adjustments for missions that actually aren't using a timer.
A suggestion to the OP that if you are going to have this thread, it would be nice to keep a list of verified bugs in the first post. This way it's organized and easy to digest instead of wading through countless posts.
Other bugs I noticed:
Missing crew callouts at the end of some missions, Nero 2 for example. (New)
Many crew combo callouts are unintelligible, low volume and almost never play in missions. (Old)
Rob