Prototypes are not as easy as you might imagine. You probably had to do a bit of filing and fettling to get your prototype to work. Perhaps a few tweaks to ensure a perfect geometric fit.
But did you update your drawings to reflect those changes? If not, your poor machining company may have been working from outdated and inaccurate drawings.
Our experienced engineers get lots of calls and emails from manufacturers who are in this situation. They need help to fix the problem (along with other issues they haven’t discovered yet).