It's a common practice, for example, to x-ray a critical piece of structure to verify it's free of cracks. A similar inspection would generally show if the hidden internals of a printed object conform to the original design.
Auditing the output of a compiler, on the other hand, would be devilishly hard, multiplied by the fact that every program it has ever produced is suspect. Given that this might include your kernel, filesystem, network drivers, etc., it's hard to find an adequate 3D printer parallel. Yes, a bit of crucial structure might be compromised by a pwned printer, but it would probably be relatively easy to spot.
Again, I wasn't meaning this to be air tight. Just more doable than nothing.
Regardless, I thought it keyed into this idea, because so long as you had it in the printer to make it such that any printer it created also did this, it fits this description perfectly. (And yeah, I realize I just jumped from 3d printer to replicators. My knowledge in this area is as shallow as it seems. :) )
Edit: forgot to add, the idea was originally that the printer would make the gun in such a way that it would be identifiable as coming from that printer. Not that it would have to refuse to make them.
edit: I hate having to ask, but instead of downvoting, are there actual reasons this fear is completely unwarranted?