Hi, I have a Big Shot and was having the same problem. I fixed it by shortening the stroke on the Bonus Unit (under the play field) solenoid. The stroke was too long and occasionally it was advancing two teeth, which whacked it out.

Before you adjust anything, push the solenoid plunger all the way in, as far as you can, by hand and see if it jumps two teeth. Do it multiple times. If it does jump two teeth you need to loosen the screws holding the coil and move it a little in the direction of the end of the plunger. If you push the plunger in and notice it occasionally does not advance a tooth, lengthen the stroke.

Make small adjustments and try again pressing by hand. Once I got it adjusted a couple of problems went away. Not only did it count balls correctly but it quit the double reset on the drop targets which was preventing it from advancing to the next ball. I've never experienced such a fragile machine! Of course, I don't have a lot of experience, so that isn't saying much!