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There is no OCR phase in Calibre, but some of the source documents people use are rtf/txt/html files generated directly from OCR conversion software. Depending on the quality of the OCR software there can be a variety of issues.
I've actually been scanning some favorite paperbooks that aren't available electronically lately, I think I'm going to add a special Heuristics function just for cleaning up ABBYY generated html - it's not fun going through it by hand, that's for sure.
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