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A lot of files fail because they're using xhtml that doesn't precisely comply with the relevant specification. Most of these errors are trivial at the moment, but may become non-trivial in the future as the xhtml spec evolves.
The purpose of the spec is to make sure that you'll be able to read your epubs on future devices as well as the ones you have now, so yes, it's a good idea to make sure they're compliant.
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