Not sure what a horn is, but it sounds like your 100,000 point relays are firing early. Does a new 100,000 point light come on too when you see the problem? Does the corresponding 100,000 point relay fire when you see extra ball at 30k points? If so have a look at this part of the schematic from ipdb.org.
Capt Fantastic 100k relays (resized).jpg
Each player has its own 100,000 point relay, shown at the bottom of the schematic, and each relay has an identical circuit. The player 2 circuit is highlighted in red. Working from the top down, what should happen is that a Normlly Open switch on player 2's 10k score reel closes when player 2 reaches 90k. Then the next time player 2's 10k score reel fires, its End of Stroke switch closes the Make/Break switch which closes the circuit to player 2's 100k relay. If player 2's 100k relay hasn't already fired, the Make/Break switch also closes the circuit to the Over The Top Delay relay which probably fires the horn or buzzer or whatever this game does at 100k points.

What's probably happening in your case is that the first switch at the top (the 10k score reel 9th position switch) is closing at positions other than 9, or there's some kind of short that makes it look closed.

If the horn/buzzer doesn't go off at the same time as the 100k relay, the Make/Break switch may be closing one side more reliably than the other.

/Mark

There's a lot of math that goes into the point level award for extra ball or credit:
Capt Fantastic Extra Ball (resized).jpg
If the Extra Ball relay works for hitting certain targets then we can assume that the rest of the circuit (not shown) is working and that presumably the top and right side of the schematic are working too. (Can you verify that the left bottom lane awards an Extra Ball when you do whatever needs to be done there?)

That leaves the big mess of point calculations in the middle. Since it doesn't work for any player, the most likely candidate is the switch that all players have in common, the 1000 point relay switch in the red box.