Missing thought or paragraph breaks. Is a paragraph unusually long? Does a scene change occur without <hr/>? They might have been lost during transcription.
Errors caused by the S.E. toolset. Tools like se british2american or even se typogrify can cause unexpected typography errors like quotation marks curled in the wrong direction, or dashes spaced incorrectly.
Archaic spellings. Is a particular word spelled in a surprising way? Mark it to check if it should be modernized. The Google Books Ngram Viewer is a great tool to get an idea of whether a word used to be spelled one way, but isn’t spelled that way anymore. Remember to change spellings in their own commits, prefaced with [Editorial]!
Printer’s errors. Before the computer age, hand-written manuscripts were sent to printers, whose job it was to lay the book out in lead blocks of type. During this process, the printer may have accidentally introduced their own typos, which are usually obvious errors in punctuation, spelling, or grammar. If you spot an obvious error like this that is present in both the transcription and the page scans, it may be a printer’s error that should be corrected in an [Editorial] commit.
There are some things that you don’t have to worry much about when proofreading:
Spelling errors. Actual spelling errors are very rare. If a word appears to be misspelled, it’s worth it to check the page scans, but such cases are often done on purpose by the author, or using a older spelling, or are spelled differently in en-US vs. en-GB.
Changing from en-GB to en-US or vice versa. Spelling differences between the continents were not yet settled then, so it's common for books to be set in a blend of spellings. We don’t convert from one style to the other, or try to ensure perfect consistency between styles.
Keeping a 100% faithful representation of a print page layout. Sometimes books have complicated page layouts in print. But ebooks are not the same as print books, with the most important distinction being that there is no “page” to align items to. So, we’re not so concerned with maintaining a pixel-perfect reproduction of print layouts; rather, we wish to adapt print layouts as best we can to the ebook medium.