I had similar issues in large assemblies once I started using connections and mechanisim heavily. I got a bunch of yellow lights and sometimes a double regen would clear them, sometimes not. I never did find a root cause for this and always thought it was just a quirk once you start pinning and slotting stuff. I found that occasionally mechanism, or things bound by connections, would cause pro to go batty and things would just start puking or doing stupid stuff without reason, this yellow light thing was one of them. I would never get a red over anything I didn't cause so, for me if the light is green or yellow I just plod on.
hth