If I have a business account in the name of say "Intermountain Headache Clinic" that has a bunch of different doctors that work for the clinic and some of the checks deposited into this account are made payable to the individual doctors rather than to the clinic - shouldn't the doctors be endorsing the checks indivdually? Right now the branch is allowing them to just put an endorsement stamp on the checks and not obtaining signatures. Any thoughts?

If the doctors ever claim that they never received benefit from the checks made payable to them, the bank is going to be on the hook.

My thoughts exactly - thanks for confirming them for me!