Same thing on my entry, confirming it.
I ticked only the second option, AI Assisted less than 50%, and the form would not let it through. It kept asking for the next box until all three were checked, so I was forced to tick the three of them. Unticking the other two afterwards and saving does not hold either: after a reload the three are checked again.
For the record, on my game everything is human made except the character voice over, which is AI generated (ElevenLabs, commercial licence). Level design, code, writing and music are hand made.
One way to see the problem from the outside: on a submission page the Genre block only lists the genres actually ticked, so when the Ai Usage block lists all three, all three really were saved.
I left a note in the free text field to explain, since that is the only place the form lets you write anything. Worth fixing before more entries come in, as Mostly AI Generated is not a label anyone wants by accident.