Navmap is EPUB3 specific.
your message says it is broken - incomplete (possibly premature closure of a Tag, making the rest appear extraneous.
Open the NavMap with a 'programmers editor' the colorizes key elements.
(Calibres Editor (T) will do this).
Everything will be INSIDE a pair of tags. The outer most is at the start, and CLOSES near the end. Someplace in the file, this got broken. you need to locate it.
You posted in EPUB Merge. ARE ALL merged parts EPUB3? You might need to make them all the same (eg EPUB2) before merging