I can't make any more progress! I'm stuck in the mine because the doctor won't stop following me around!
She won't let me fight the plant monster in the main chamber and she won't let me leave her anywhere!

I have the same problem - is there still no solution after four years? :-)

Stuck in the same way, amazing, can't progress and even loading a previous save, doesn't change it.

Since all the holes i'm searching are missing the drill bit that supposedly is in the hole south of the miner anyway, so that's great.

EDIT: Oh it doesn't matter anyway, even if you solve this there's an other glitch that makes your generator run out of oil even if you close it, great.

EDIT 2 (SOLUTION):
So i've finished the mine, i had to reload a previous save, there's way out of the doctor if you get her early.
You need to get one character at a time, get the stuff for the soldier bring him where he needs to, then bring the doctor to the man in the elevator and do the stuff there, than the electrician.

If you don't have a previous save, that's unwise when playing any game with RPG elements.

If you finish the the fuel in the spray and the generator doesn't make anymore, you'll find bottles full of it, one you have to save for the drill.

So that's how you have to go about it. I'm glad i figured it out because the medium play time of this is of about 1h.

I get to be in the cool kids club when i finish this. ahahahahah