Ok, I went back and looked into it. I was not using mirror symmetry but it's still doing it.
To be perfectly clear. I'm very new to this site and haven't figured out how to attach pictures on here yet (I know... I'm dumb, I'm sorry). Nut I'll try to explain the best I can in the meantime.
I have a MK3 cockpit with a MK3 monoprop fuselage, a liquid fuel fuselage, small cargo bay, then loading bay (all MK3). In the front of the small cargo bay attached to the center line snap point I put a small stack decoupler (in line with the ship) then the rover is attached to the decouple inside the cargo bay. Again, no mirror symmety is applied.