There is no doubt that compressing a whole industrial supply network into a little probe is incredibly hard.
But I can't see microgravity specifically as a huge challenge. If you can get a probe to another star system, you can probably figure out how to spin it.
I suppose it depends if you're assuming the probe is a complete factory, just taking in regolith and spitting out new probes, vs if the probe deploys and builds up the factory on the surface of an asteroid.
In the latter case spinning doesn't get you far.