A frequency analysis reports shoes 40 times and shoes, 12 times as separate entries. The real count is 52, and every conclusion drawn from the split numbers is understated.
The effect on analysis
Punctuation fragments counts across variants of the same word. On a large text this systematically understates the terms that appear most often — precisely the ones the analysis exists to identify.
Normalise before counting
Strip punctuation, fold case, and collapse whitespace before any frequency work. The counts then reflect the text rather than its typography.
Know what you are discarding
Apostrophes and hyphens carry meaning. Stripping them turns don't into dont and state-of-the-art into three words. That is usually acceptable for counting, and it is worth knowing it happened before quoting a figure.
Try it: Remove Punctuation on SeoWolf's Notepad.