On Fincen form 104 if we check box d "multiple transactions" in section B do we also need to check box c "multiple transactions" in line 1?

Yes

If that is your excuse for not completing Section B.

Good point cbinder. If there was multiple transactions, box 1c will always be checked and Section B box b will only be checked if Section B is left blank or is incomplete.

Has anyone ever been written up by examiners for checking the box even when Section B was completed?

Hard to say since that is not public information. At best it is a techincal completion error and unless you had a lot of such errors, technical completion errors seldom make an exam report. You might get some pretty strong words in your exit conference to improve your CTR quality.