Go into coil test one back and remove the balls with the program.
Go into switch test and drop the balls in one at a time to see if they all register in the trough.
If they do exit test and start game, if they don't then reseat the connectors on the trough boards and repeat test.
On game start it should load two balls into the VUKs off of the subway and stage the third one in the shooter lane.
If it keeps trying to load balls then you have a bad opto or a stuck/broken diverter in the subway.
Also check the switch in the shooter lane, if it is out of adjustment or bad the game will keep trying to stage a ball.

Copied this from an old thread on this subject. I had the same problem a while ago.

If this does not work google search STTNG pinball Balls keep loading. There are several old posts on this very subject. I believe I ended up replacing a board under the play field to stop my issue. Good hunting