If you are absolutely sure that it is in straight and not at an angle, its not all that unusual for the screw hole to not line up right. I frequently have to 'persuade' it to line up, so yes, it sometimes will be under a little bit of pressure.
If you're only off by a millimeter, you're fine to just gently coax it into position. Just make sure you aren't hung up on anything else. Look along the edge of the slot and make sure the card is in evenly first.
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