The game wants to load a ball into each side of the subway. If the diverter underneath is broken the it can't get a ball into each of the three locations. I would start there. The symptom of that would be that it loads a ball, the diverter won't fire so the ball ends up behind another ball on the wrong area, game kicks it out and repeats. It could also be a subway switch but then it's less likely to keep kicking the same ball out in my opinion. But check those aswell.

I would bet it is an issue with the trough optos. I loose connection could be the culprit.

I agree, loose connector, or if the connectors are still IDC a loose or broken wire. Have had weird phantom trough issues on mine due to that connector. Still need to replace some day.

Sounds like a flaky opto somewhere...first thought would also be the ball trough.

Is it the original ball trough boards. If so they are pretty notorious for failing du to the vibration of the balls in the trough ( I think Williams used a new board for their widebodys at the time and they failed often enough).

There is a trick to minimize the vibration on the boards by lining the screw holes with a rubber ring acting a shock....but personally I would just buy new boards from Great Lakes Modular:
https://nestlepurelifedirect.com/pages/signin.aspx

Look for the williams widebody trough boards set.

If it's not the trough boards it likely is the optos on the underground subway...you have one going on and off which could be a bad opto solder or it just slowly dying. Harder to troubleshoot so just keep cheking those underground optos when it fails next.

But I would start with the ball trough.

Try putting all 6 balls back into the playfield and into the trough and see if it correctly loads 3 or if it starts having problems again. I'm not convinced its just an opto, although it could be. I think trough opto symptom might be different than this.

Yes start there, if it is not loading to the VUK's correctly something is wrong. Make sure you check/test the subway diverter action in coil test, make sure it is firing. Go through the optos, go into test mode and let it sit for a few minutes and see if any go off on their own. Then run balls into the trough one at a time and watch the switches trigger, once loaded wait another minute or two and see if any of those go off on their own. All optos have to be working correctly for STTNG or it can do wacky things. Clean them all anyways next time you have the PF up.

When this happened to me, I had a blown fuse that controlled the top diverter in the subway.

Thanks everyone for all the great ideas. As that is what mines doing now.