Most likely an "href" bug. But, also check spelling. opf/xhtml relations are case sensitive.
opf might have, for example... Cover_p
The actual xhtml file might have... Cover_P
This will show as two errors, one will be an unreachable, the other will be an unused. Fire your epub through a validator, Sigil has a fairly good one and it will let you double click the errors and take you to the appropriate file and highlight the line it doesn't like. If you don't get an error then try regenerating your TOC with sigil, it's all tick boxes, dead easy. This will create a nice new clean NCX file for you. (Remember to make a back-up before you start fiddling.