Check that you are getting free and easy movement of the print head carriage on the rails. If the rails bind, then the motors will do some funky things. It should be difficult to get the Y axis smooth rods in without them being parallel, but it may be possible in some instances. It’s also possible to damage the linear bearings. One of mine was messed up, and I’ve replaced it with an LM8UU bearing that I had around the house from other printer projects. With the printer power off, it should be quite easy to move the print head around in the X/Y plane.