Read this: http://www.pinrepair.com/em/index2.htm#steps

Would have to see the schematic if it's not the unit.

First I'd double check that you're only getting a single decrement pulse to the credit unit either by watching it carefully when you (have someone else) hit the credit button, or using a lamp tester.

If you're satisfied that there's just one subtract pulse have a close look at the decrement lever arm pointed to in the bottom half of this photo:
Credit unit (resized).jpg
The top half shows the credit unit at rest and the bottom half shows the decrement arm activated at the start of a step down. The short horizontal arm drops between the teeth of the gear to keep if from stepping down more than one step. That small arm should move very easily back and forth around the shoulder bolt pivot on the right end. If that arm is binding somehow you might see multiple credits subtracted because it takes that arm longer than it should to drop between the gear teeth. The video of this stepping process is at www.funwithpinball.com/small-boards#CreditUnit

/Mark

Lever arm sticking or the clock spring wound incorrectly.

It can also be the increment arm that follows the teeth. If this one is stuck as soon as you go to increment it drops all the way back to zero.

I usually use 4 turns on Gottlieb stepper springs like this one. Start with the spring completely relaxed, then wind the loose end around the axle 4 times before fixing it to its anchor.