I just manually manipulated it back into place. Not sure why this happened, do the limits not work with the cartesian and tool coordinate methods of m...

@johann-voigtlander It was, and I had tightened it super tight, but still slipped. I put some bearing compound on it and that fixed it so far.

@matt_d the rods are slipping for me when using the J5 motor (i have put the set screws). Do you have this problem too?

drill it out with a 3mm bit. I had the same issue.