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It's very unlikely that this would happen if you're getting your books from reputable sources.
If you're buying your books from Amazon or a similar store, check the editor and other bibliographical data. Sometimes less-than-reputable editors just make a quick version to sell based on public domain texts with little or no regard for the quality.
If you're downloading ebooks for free make sure the source is reputable as well. Sites like gutenberg.org tend to be good for this purpose.
An important note: if you have a preference for a specific editor or translator, make sure it's the same on the ebook you're downloading. On stores you'll usually find this under bibliographic data. Sometimes translations can be very different between them, so if you like a specific translation you should make sure that's the one you're getting.
Regarding the fact that ebooks may not be accurate since they're made by people based on paper books, that is a risk that exists for any and all books. Even paper books. This is especially true of older books. Unless you're getting a facsimile edition, if you buy a recent edition of an older book, it's very likely that someone put together that edition to adjust to new printing methods based on older books. In some cases you'll even have different versions of print books depending on which sources they're based on (one such example is Shakespeare, as depending on the quarto or folio that the edition is based on, the text itself can be very different). If you're particularly interested in getting a more complete picture, some editors (mainly academic-oriented ones) often have different editions of works that will be based on one source but note where other sources differ and include the variation for reference purposes. For the average reader, though, it's usually just enough to research what the "standard" or more accepted version for a given work is.
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