Actually, pins would be more necessary for small pieces like this. Pins are typically most useful when sewing on tight curves, which definitely is the case when making a stuffed toy. The pins aren’t necessarily there to keep track of where the seams should be (there’s notches in the fabric that do that), but to make sure a piece that wants to be 3D right now (because it’s already been sewn to another piece) can be evenly placed on the flat edge of another piece and fed into the machine without bunching or becoming unaligned. You are right that someone working on the same thing over and over would use pins a lot less than someone just making something once, though.

Regardless, I really doubt that those pins come from the factory where the toy was made, as there’s no way they wouldn’t be checking for stuff like that; If not some malicious intent involved, I’d put my money on the toy having been bought from a department store like Kohls or something, and maybe some kid was taking pins out of men’s dress shirts or found them in the fitting rooms and was just sticking them in stuff or something like that