Give your ePub another check with epubcheck 3.0.1. Version 4.0.0 is in alpha release and could have problems with it. I cannot' say it does for sure or not, but given that it's not yet out of alpha testing, I would stick with the 3.0.1 release.
But from the error you mentioned, it sounds like your OPF file has too many entries in the spine. It would help if you could post a copy of your OPF file.
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