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This has been happening for some recent Upper Deck scans...I've been carefully placing the cards 

tightly on the edge of the scanner, expecting perfect alignment for cropping.   For some of the cards

the crop rectangle aligns perfectly.  For others, not.  The edge crop line where the card was placed

on the edge of the scanner aligns with the card, but the four corner dots cannot all be dropped on the

corners of the card.  It seems like the card is not an exact rectangle shape, slightly off centre. 

 Is this unusual or am I going wrong somewhere,

I kind of think that the issue may be if you are lowering the lid it is shifting the card so slightly it is now not perfectly aligned to the edge.

You have to find a good editing software with which you can make 'fine rotations' to align your card to right angles no matter how crooked your scan is. 

This is important for when you have a round item, such as a coin or 'pog' etc. 

The software I use that has this function and other easy useful functions is called Irfanview.

Photoscape is pretty darn good with alignment and it's free.

Eriquious and vrooomed are right. fwiw, when I place cards on a scanner, I don't worry about them being straight. And I never put them at the edge. I just scan the card and then take the time to use either Irfanview or Photoscape X to get perfect aligned card images. And I've never had a card image flagged or rejected.

I agree with what the previous replies have to say about image straightening, but to answer the OP question: Yes, I have quite a few cards where the edges do not meet at 90 degree angles.  The card ends up being a parallelogram rather than a rectangle.

-Tom