hmm not wrote in here for a while and haven't played the game for a couple of years, but i'll have a stab at the questions for you.

1, I have seen it happen sometimes, did you order them to do a mission?
2, Never seen this happen, could be new.
3, Resupply birds getting stuck as been in the game since the start, I assume it's probably got something to do with the landing pads they were originally given in the resup order are now occupied by craft produced at the airfield hanger.
4, again been in the since the start, possibly due to only targeting the en if they themselves get targeted by the en craft, maybe the code should be looked at to ensure if en units stray into the radar range of the craft they will get targeted by the unit AA in the area, (most probably a AI issue)
5, At least they are getting destroyed unlike the ones that endlessly loop into the sky or lawn dart into the ground and do not explode causing further resup problems/cap missions later on due to the game still seeing them as being active.

Phil

You need to give your wingman/flight a "weapons free", "help me", or "attack my target" command. Once the threat is dealt with give hime a "weapons hold" and "rejoin formation" command.

Also AI Heli wont engage with guns, so if you inside minimum weapon range they wont fire. Sometimes in this situation you may find yourself in the unfortunate predicament where two KA52 are following you at close range. As soon as you are a safe distance they will blow you out of the sky. Its a shame they dont use guns, as AI are a sitting duck in close for the Apache. Ive read heli AI guns were functional in EEAH but for some reason not in later builds.

If you fly a resupply, recon, insertion, missions the lead helicopter must not outrun the flight, and the lead must input selected waypoints. If you dont they will stop at the active waypoint and wait for you. On the approach to target select waypoint "X" If you dont then troops wont disembark, resupply wont complete, recon will fail. Best advise is to maintain formation, and monitor/input selected waypoint.

eg: once I flew an insertion mission into a very hot LZ. I was in the Lead BlackHawk and I had a couple of AI Commanches in tow. On the approach to LZ there was a large flight of KA52 inbound, so I direct my commanches one at each KA52 directing traffic from a safe position. The plan being that I could insert troops while the Commnanches kept the KA52's busy. Well this worked great except my troops would not disembark. This is when I selected waypoint "X" then directed the flight to "rejoin formation". As soon as I did this my troops disembarked double time

One other thing worth noting is after you recieve a "mission complete" its pointless re-arming and continuing the mission. In fact I think it bugs the campaign. If you want a long mission where you can continuously re-arm at differant places, then choose a mission where you can avoid a mission complete, like a transfer mission, or CAP. These missions can be hi-jacked, re-armed, used used for an ongoing engagements as long as you use other FARPS to re-arm. By other FARPS I mean stay well clear of Way point "W". If you approach your home farp then mission will most likly complete or fail.

Proxitity to target with the above mentioned missions is also critical for mission success

eg:
recon= 2.5km from "X"
insertion= 30m from "X"

Remember not all percieved bugs in this game are bugs, If your in the lead helicopter, you may be the bug

Do you have any tacview logs which shows the problems you describe? It makes it easier to analyze if we can see what is happening. E.g. if the AA-units never fire, or they fire sometimes, and then maybe run out of amunition.