Maybe test your subway switches? I had an issue with one of mine not registering regularly which was causing some questionable behavior similar to what you are describing.

I ended up replacing my flakey switch with an MRS switch and it made a world of difference.

Got it, I missed that part.

Actually, this makes sense. There are 2 subway switches and if the right side from Ethyl is not registering regularly, it will think you hit the left scoop as finnflash suggested. The other subway switch is the one for the middle subway entrance and that is the switch that rarely would register on my game. When my switch was not working, I had the exact same thing happening when I would shoot the center subway entrance, it would say NOT HERE and think I hit the left scoop. I also could rarely activate the mystery award light due to my switch not working.

I believe the Pit Creature mode reads from the subway switches, not the upper optos. So even if your optos are 100% working under the crypt, that does not matter when it comes to searching for the Pit Creature. I would suspect your subway switch on the right side.

Glad to hear you got it working. If the switch gives you more problems in the future, consider the MRS switches that Sonic makes. It is a one-time fix and they work great!