From how you describe it, I think I have seen the same. Take it all apart and start again... It will go back together properly, but it’s almost as if the steerer pushed things out of alignment if allowed. Take your time and be very careful when assembling the steerer onto the fork. You may need to do things in a slightly different order to the service manual and keep offering up the fork, to check things are good. Patience is a virtue :)

There may be a small gap at the back of the ‘triangle’ where the stem mates to the fork, but the 2 faces should be in contact. If you see daylight, keep trying. Do not try and use torque to get it to seat!

I hope that makes sense.

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Developing aero, fit and other fun stuff at Red is Faster