I think not putting an auto-plunge in Star Wars Episode One was a pretty foolish blunder. I wouldn't say that it literally makes no sense, it's an understandable mistake to make, I suppose.
Some Data East games have two scoops for no reason, which I'd say is bad game design.
It doesn't make sense that the most recent code update for JJP PotC is still only available under the counter and isn't on the website yet.
It doesn't make sense to put pop bumpers in your game and not have them do anything interesting besides knock the ball away.
The upper flipper on Hotdoggin' doesn't make sense.
It doesn't make sense to base a pinball machine off of a movie that hasn't come out yet and might bomb. (although this changes somewhat if it's a movie that's part of an iconic franchise)
It doesn't make sense to give up the Legend of Zelda license to go after American Gladiators instead.
It doesn't make sense for a family entertainment center to have five pinball machines that are all in disrepair and unplayable when they could sell one and use the proceeds to hire someone to repair the rest.
It doesn't make sense for an operator to comment that they are planning on sending someone over to repair a broken pinball machine on pinballmap and then not do it for over a month.
It doesn't make sense for a player's heart to fill with loathing when the referee at a pinball tournament makes one singular call that they disagree with, but it happens. Too often.