What is the original media source? Camera? Phone? What make/model? What is the wrapper and codec?
We can only make wild guesses without this information.
Yes, theoretically, it could be a variable frame rate issue. This is not a PPro malfunction.
Dell Precision T7600 (x2)
Win 7 64-bit
Adobe CC 2017.1 (as of 8/2017)
256GB SSD system drive
4 internal media drives RAID 5
Typically cutting short form from UHD MP4, HD MP4, and HD P2 MXF.