Pem size changing without warning

I just had a big issue with toolbox/pem changing size of some pem studs from the 8-32 size to 5/16-18 size. This turned into a big issue since the shop made the parts to the larger size. Any ideas why this happened. I did chang the size of some other pems in the same main assembly but not in this subassembly. Note this main assembly was made from a packngo of another asssembly.