[wheelsup_cavu]

I don't know if this one is new, but sometime, when switching to autopilot, it restarts the checkpoint, so your plane is going to the previous waypoint all the way back. (Pacific Fighter)

Unless you use Auotopilot to follow the waypoint path you will miss some of the waypoints. Once you turn the autopilot back on you will go back to the first waypoint you missed and start following the waypoint path again.
The only way around it is to be the flight leader and use the radio messages to tell your flight to go to the next waypoint when you realize you are backtracking.

Some enemies are spawning in each others at enemy base. = Explosion

This is most likely a timing issue. One flight has not cleared the runway before the next flight is spawned into the runway to take off. The only solution for this problem is to alter the .mis file.

Allies are following in suicide Operation (like going into an enemy base). They are killed by the flak.

Yep, the AI are nothing if not suicidal when they lock onto a target.

Wheels