If you sent them current transcripts, as you should have, they will most likely insert the grade when they verify your application. If for some reason they don't, you can submit an "Academic Change Request" after you receive your verified grades, in which you describe the error and ask them to correct it.
I remember reading on the website that the ACR process may take up to a couple of weeks to complete; however, since it's still early in the application season, it would hopefully be much faster if you had to resort to this.
AMCAS "fixes" all sorts of things when they verify your app, and it's no big deal. In my case, they added AP credits that my college never actually gave me credit for (except the right to skip introductory courses in certain subjects), but this had no effect on my GPA.
On the other hand, the verifier really screwed up my grades from B-school. I went to a school that grades H/HP/P/LP/F (Honors/High Pass/Pass/Low Pass/Fail), which the AMCAS website itself says is equivalent to ABCDF, but the reviewer classified everything as Pass/Fail, giving me a grad GPA of NA instead of 3.8. But I decided not to fight it, because I was told that med schools pay no attention to grad/profl grades anyway.
