Ok on mission 3 most of the ships are from the original Star Fury game which I did not change. So, the only ones to fix were mine. I loaded them into “Slot modder” and found six that the slots touched either the top or bottom of the edges. I was not aware that this could be an issue until now, but as rstaats10 pointed out, easy to fix.
Later tonight I will edit the main Mod and will post it as Multiverse 1.01.
But for those that already have the Mod I am posting the edited correction. It is only one text file: Main_ComponentConfigurationSlotsEnemy.txt
Download and place it on the Multiverse-1 campaign.
http://www.shrapnelcommunity.com/thr...?Number=570415
Hope this works!