How many balls are there supposed to be in the machine?

You tested the ball through and the shooter lane switch with a ball?

Well, let's look at your question... "why?"
Mike has the "what" so why would the game kick out two balls instead of one after locking one in play?

Usually it's because the game is not seeing the ball in the shooter lane groove. It will keep kicking out balls until that damned shooter lane switch tells it "Ok a ball is here, thanks, ready to shoot!"

So that's the first thing I would check and like Mike says check it in test mode with a BALL... not your finger, please

Next it *could* be a trough switch that's stuck on so the game thinks it still has two balls in the trough and will keep kicking trying to get them out and into the shooter lane. This doesn't sound quite like your problem though or you would have told us that the kicker keeps kicking even though two balls are out. If a switch in the trough weren't registering the game just wouldn't even start so much less likely that's a problem either.

So we're back at the shooter lane switch. Check with ball, report back.