So we just tested a lot of mission files I made to rule out the following as issues:
Tested with no carrier settings(TCN / ICLS / L4 / ACLS) and with all settings - no change
Tested with and without copies and pasted aircraft - no change
Tested with and without AI ships and aircraft - no change
Tested identical unit setup with all carrier settings enabled but on Caucuses - worked as it should.
Conclusion is pointing towards something on Mariana causing the issue, I don't know what it might be - Radio Frequencies? ADF? TACAN? Hope this at least gives you something to look at.
Matt Glover's post in F5E Remastered is giving missions a false tag was marked as the answer