I just built my new computer and i was installing the motherboard and when it came to install the last screw, the standoff was a few mm's out of place, so i grabbed a smaller screw and put it in there and it fits nice and snug. Is this ok? its not loose or anything.
Agreed. I wouldn't be too worried about it, but if it does concern you, it probably just means that you tightened the other screws too much. You can try loosening the other screws to see if that gives you a bit more wiggle room to fit the original screw and then, once in place, tighten them all.