I've encountered this error and created a stripped-down version of the original EPUB that still exhibits the error: invalidUtf8Sequence.epub

For this file, EPUBCheck v5.1.0 reports

Validating using EPUB version 3.3 rules.
FATAL(RSC-016): invalidUtf8Sequence.epub/OEBPS/html/Chapter_6.xhtml(88,792): Fatal Error while parsing file: Invalid byte 2 of 4-byte UTF-8 sequence.
[...]

I believe this is a false positive. At least I can't find anything wrong with the HTML file.