Another thought - deformation is usually caused by over tightening the stem; which makes the steerer tube *expand*. that sometimes makes it harder to get the fork out of the frame (DAMHIK), but should actually make it easier to get the quill in the steerer.

So I am thinking wrong size stem (ie too large), friction from rust in the steerer tube, or burrs on the stem.

Best to measure the stem OD and steerer ID with a decent micrometer to eliminate the first issue, then I would clean up both the stem and the inside of the steerer tube and try again. Don't forget anti-seize.