When I was in college, I had a teacher that pulled some shit like this on a big final project I did. This was a project that constituted a huge percentage of my grade. My actual score, as graded by the TA, was ~95 out of 100. The teacher decided to discount it to something close to ~15 out of 100 because of some technicalities about the structure of her class.

I took it to the dean, and he reversed the teacher's decision. My final grade, which was going to be a C-, turned into a solid A.

The moral is, take it to the dean. The worst that can happen is he does nothing and all you lose a couple hours trying.