I am an exempt employee paid every two weeks. If I work 40+ hours I get the same pay, however I have had a couple weeks where I have totalled 38 hours in a week due to doctors appointments. The company still does not pay for the full 40 even if I have put in extra time in the other pay period week. Is this legal?

As an exempt employee, the employer cannot "dock" partial day absences. The DOL allows employers to apply PTO for missed time. In the case where no PTO is available, the employer cannot "dock" portions of a day.

The exceptions that I am aware of are for "full" day absences. In this case, the employer is permitted to "dock" wages. Another exception falls under FMLA. An employer may "dock" partial day absences if the absence is covered by a restricted work schedule with a qualifying FMLA event.

My guess is that this is not FMLA related. I'd suggest filing a claim for unrecovered wages with your local DOL office.