In the past, I have noticed a spelling error maybe once or twice in an entire eBook. This one however, was a fountain of errors. And they did seem to get worse as the book went on (maybe I had just been sensitized to them after having waded through so many).
I don't go for the "software not compatible" argument. If there is an electronic version of a book used for printing, I see no reason why that can't easily be converted to a different format. I've done data conversions like this for a living for decades, writing software to convert stuff. You have the text of the novel, then you have formatting/markup that presents that text in a certain way. You can try to "convert" the formatting/markup if you want, or you can discard it totally and start anew from the raw text. Then you proofread the result when you are done, possibly making manual corrections if you find that your conversion algorithm was not 100%. If you're too cheap/lazy to do that, then your books belong in the bargain bin, not sold at full price. It would be nice to post a warning at the front of the eBook, but I doubt many authors are going to put "Warning, this eBook started from OCR, was not proofread, and may be a steaming heap of garbage in the presentation department".
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