Plot hole: Scully's statement that she was 23 when she wrote her senior thesis in college throws off her timeline of college, med school, residency, FBI Academy, Quantico teaching assignment for two years, and X-Files assignment at 28. Her undergraduate degree in Physics should have been completed when she was 20 or 21 to allow at least 4 or 5 years for her medical training.
Plot hole: Eddie's ability to shape-shift is attributed to every muscle in his body being striated. While that's a reasonable explanation as to how he can change his face, it doesn't explain how he is able to change his hair. He has short hair and is balding, but when he mimics Mulder, he is able to match Mulder's longer and thicker full head of hair.
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