Hey, 

first of all, I'm still in love with this tool. I've flown around 500 missions with it so far. 

I tried something new by playing a USN campaign, as I normally fly German planes. In the first mission on the Midway campaign, one whole squadron of Wildcats get spawned on the Eastern island without a runway and the first few planes of that squad are spawned in the ocean. Is there a runway or carrier missing? Thanks!

Second mission was a massed attack on the IJN carrier group. Unfortunately, something went wrong with the spawns for some units and many collided mid-air immediately. Also my autopilot (filthy casual, I know) collided with a squadmate, something I haven't seen before. 

Do you have an idea of how I can fix this? I didn't have this issue that often with Eastern Front campaigns

Past reports of this kind of behaviour usually have to do with using a mod.  Are you using one?

If so, it may be the configuration of loadouts.  A loadout has been selected for a plane type that can't use it.  This sometimes happens even with non-modded games - if I don't catch the change in the latest patch or add one incorrectly to the payload tables, it can happen. 

If you upload/post the mission file here, I can have a look.