Once you progress in multiball after locking 2 balls the optos will start to complete the matrix for you, and if you have doctor 7 selected, will complete the whole board without you earning it.

It's likely a combination of the opto boards (cracked connections are common here) and maybe a warped opto carrier.... it's plastic and distorts over time (from who knows what.... I just replaced mine).

That's the good news. The bad news is you have to remove the mini playfield assembly to replace, and that's a PITA thanks to the older style playfield tilt in that game (no slide rails). You have to take off the glass molding at the top of the game, put the playfield up, disconnect the harness, loosen some screws, and angle it out.

https://www.afpinball.com/uploads/7/4/1/4/74144281/thedoctorwhominiplayfieldv1.2.pdf

is a great guide to servicing the mini pf