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They are probably "soft hyphens" which are a way of indicating places where it is possible to break a word across lines, but should be hidden otherwise. As you see, not all applications know how to deal with them, and I find they are generally overkill. I don't know if you can prevent FineReader from adding them, but I guess you can remove them with search and replace (but note that some of the hyphens should stay).
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