Recently had a few EPUBs returned from a client due to them failing Apple's Transporter checks.

I realise now that through my hand editing some content was commented out from the OPF but not removed from the package folders.

I had checked using Pagina EPUB-Checker 2.0.10 (EPUBCheck 5.1.0) and Pagina EPUB-Checker 2.0.9 (EPUBCheck 5.0.1) and had not had any flagged warnings. The issue IS flagged as a warning in EPUB-Checker 2.0.9 (EPUBCheck 4.2.6).

I have had a look at the release documentation here for EPUBCheck 5 but didn't see a reference to this, so have I (and Apple…) missed the fact that extra files in an EPUB package are no longer raising a warning in EPUBCheck?… or is there an issue with EPUBcheck? or an issue with Pagina's implementation of it?