Do not force anything.
Motherboard holes and motherboard standoffs have a definitive standard placement.
Without the I/o backplate installed, see of the holes are lined up.
I would be surprised if they were not.
If only one is off, ignore it; not all screws need to be installed.
Possibly , your back I/o plate is not fully inserted.
Or, when installing the motherboard, you need to press the motherboard I/o section to the back plate.