It's a slippery slope here. If it's shorter than the other rounds from the same box, don't use it. You cannot compare it to rounds from other boxes.
Take the same amount of powder, cram it into a smaller space and you get more pressure. That pressure increases at an exponential rate. In a situation like you have, set back becomes critical. You can't compare it to other rounds because they have different load recipes.
What happened is a .380 case somehow got in the 9mm production line. Because all the dimensions are the same, except case length, it went through without anyone noticing. Because it's shorter, I'll bet the crimp isn't that great. A not as tight crimp would reduce the amount of pressure built, but there's no way to know how much.
Would the round you have been too much pressure in your gun? I have no idea. The only way to tell is to fire it. It probably would have been OK. Since you caught it, why take chances?
I had a similar thing happen to me. I found a .45GAP in a group of .45ACP rounds. It fired fine, but felt a little stronger. I probably should have just disassembled it, but I didn't and nothing happened.