This often happens when a file isn't properly formatted in the first place, or has been converted from one format to another not-so-compatible one. In many cases, working from the original file removes many of these kinds of problems.
When the original file isn't available, using find-and-replace can work, if you know how it should be formatted... but depending on the app (like Word), find-and-replace don't always work as they should, because Word obscures its formatting codes (even, apparently, to itself). I've occasionally found myself manually fixing entire books this way.
You might try converting the original file to other formats, some of which might make find-and-replace easier. Try converting it to a straight textfile, for instance, to strip out a lot of the extraneous code. If there's not a lot of stuff to put back, i.e., italics, bolds, etc, this can be easiest. Then import that into BD and use its find-and-replace to fix things.
If you know HTML, I've found it easy to import the HTML generated by BD into Dreamweaver (its find-and-replace tools are superior to BD's, IMO), fix the HTML there, then paste it back into BD.
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