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The only times I have seen something like that, it turned out that for some words, each letter was wrapped in a tag. It was usually a span, but, if part of a word is wrapped in an i tag for emphasis, it won't automatically select the full word.
If this is a bad conversion from a scan, you can get all sorts of things happening. If you open it in the calibre editor or Sigil, it will be fairly obvious if the above is happening.
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