I managed to fix this with help from Sushut's "Create a STAR SYSTEM with Kopernicus!" tutorial on youtube. He goes directly over this bug when creating planets and provides a fix that seemingly has no downsides. (Although didn't really explain at all what it does, I have no clue to be honest,)
Also thanks to Treiakuar's Rapid fire landing series so I could check which planets from the modpack had this problem more easily without having to wait for loading times.
Here's the fixed version of MPE incase anyone needs it, enjoy: https://drive.google.com/file/d/18ejwpTL2c7360p1nHh8WKsD9hUWn76cn/view?usp=sharing