Do Fall Courses Count in PhD Admission?
The easiest way to tell if fall grades will be taken into account is to look at the application instructions. If you see instructions asking you to provide your mid-year grades, then that's a pretty clear indication that they will be taken into account during the admissions process. If you are not asked to submit it, then follow that guideline. 

If it's optional for whatever reason, I would assume that you should plan as if it were a mandatory submission.