To close a business case everything has to be in balance, otherwise you get in trouble latest when you do archiving.
Looking at your examples there are some open questions.
You said the GR was done for 100 while you received 102, or done for 100 while you received 90.
Is your vendor aware of that e.g. the delivery note matches with your received quantity, just the user made a mistake?
If so, then you already can get in trouble when you receive the invoice, depends a bit on your tolerance settings.
And honestly, would you personally pay for 100 if you only get 90? would you personally ignore this case too, like you want to ignore it with doing other movements to continue with a faulty process?