Many shops have size limits on parts that can be cut on a beam saw, or run through an edge bander for example.  There should be a size limit that can be entered in the processing station. If a piece is under that size it can prompt the user to either oversize the part (and maybe add a note on the label to trim to finished size) or to not process the part. It is very painful trying to constantly monitor for small parts or add logic to each subassembly that oversizes the part if they are under a specific size.