@SpyderBlack723 Yep, there's a good chance they are being spawned in the water..
No they're being spawned on the deck of the carrier where I placed them in the 3D editor. I spawned on the carrier too when I was testing the mission. Saw the helicopters sitting on the deck with their crew inside. Opened the combat support menu and I saw the helicopters in the menu, however they were being registered as combat ineffective even though they were sitting on the deck, undamaged. I could get in them and everything too, but once inside there was also no option to talk to the pilot (because once again it thinks they're combat ineffective for some reason).
At first I figured it could've been one of the many mods, but even when running just CBA and ALiVE the issue happens. Keep I was using just the Player Combat Support Module and syncing it to the helos that had the combat support code in their init fields, I wasn't using the other module that spawns them by itself.