TLDR: MMU2 stops extruding filament once print has started.
To explain what was happening:
I had just finished a 6hr print that was using the MMU2's single mode where I select the filament for it to print with.
Everything seemed fine. I then went to start another print using the same color. The MMU2 loaded the filament like I would expect but all of a sudden it move the nozzle over, unloaded the filament and went to the next one (I have auto deplete on). I decided to stop the print and try it again.
After getting the filament loaded properly I started the print. The print would start fine but would start slipping on the hot end's extruder gear as if there was a jam. I tried some different settings unloading and loading the filament and eventually went to see if it was heat creep. After cleaning everything out I ran filament through it and it seemed fine.
Started the print again the MMU2 loaded the filament as expected, but at some point is started skipping again.
I happened to look at the MMU2 and saw that it wasnt even moving so it was holding the filament in place while the extruder was trying to do all it could to pull it through.
I eventually unhooked the MMU2 bowden tube ran some filament through it and had it think it was loading the filament took another spool and directly put it into the extruder.
I can confirm the MMU2 is not moving at all and the printer prints fine with a direct feed.
I don't know what caused this and why it is doing this, but is this something that has been reported? Now I don't even want to use it, if it may stop moving the gears again.
Keep in mind I have tried a few prints including one I know worked before the issue arose.