It happens, best way I’ve found is to put the axle in, and lightly tighten all bolts, tap the axle in several different places side to side with a rubber mallet, lightly tap the axle again from one side to the other, and repeat till bolts are tight. Alternate with the bolts also. When I say lightly, enough so it knows it’s being hit. That gets everything lined up. Also tap the bearing cassettes

Think of it like you torquing the head of a car. Start from the inside work out, starting with just tighten the down, spinning the axle between each cassette. Just like Ric is saying…

Tighten the outer bearings first with the axle in place. Use a yard stick across the bottom of the frame and measure from the bottom of the axle to the top of the yard stick (bottom of the frame) to get axle straight with the frame. Then tighten the third middle bearing. If it tightens up after tightening the third bearing drill the mounting holes in the bearing hanger bigger and try again. Are you sure the axle is not bent?

Gif

Odds are you don’t have the bearing centered well in the cassette. If they’re tight you need to align them before you tighten the axle down.