Yeah this is kind of a known bug and has to do with it trying to suck in components for a build, then immediately pushing it out (if it's over 75%). Unfortunately I'm sort of in the middle of finishing something, but I will fix this as soon as I can.

I managed to get it under control by turning off the projector and manually putting small amounts of the needed materials in until the number of construction targets was low enough that it was no longer trying to draw more than it could hold.

From my observations, it looks like the nanite factory decides what it will need to build, and pulls all the components it will need. When there's a lot of blocks under construction, it fills up.

If this is the case, I may have a solution. When the factory needs a part, it checks to see if any of that part are in its inventory. If there isn't, then it pulls a small number of those parts.

It's only really a problem when you're deconstructing. I need to make it clear inventory only when that is occuring, and leave it alone during other functions.