It's Sartander! 0% chance it's by mistake. Best thing you can do is send a second check mid-cycle and hope it limits their ability to play stupid.

I experienced the exact, same issue with Sallie-Mae and had to call monthly requesting an adjustment. I tried writing something like "Apply excess to principle" in the memo line with no success. Next I tried using pre-printed stickers with account number, loan name/group number, and apply to principle with no success. It still took calling once per month forcing them to do an adjustment. Sallie-Mae's system kept paying me forward instead of applying to principle.