We found EPUBCheck v4.2.0-rc will report errors when toc nav's order is different from spine order.
Now we found that wrong order was prohibited already in EPUB 3.0 but EPUBCheck v4.2.0-rc may be the first version to be checked properly.
(#888)

Unfortunately, we might already generate not a few EPUB files which have different toc order from spine because printed books have such toc order.

For example, our Manga content is structured like below.

[spine order]

• Chapter/Story 01
• Column 01
• Chapter/Story 02
• Column 02
  ...

[toc order]

• Chapter/Story 01
• Chapter/Story 02
  ...
• Column 01
• Column 02
  ...

Such different order of toc may be prepared because the value of chapter and column is different and such toc makes it easy for users to access to the prioritized chapters.
I'm not sure but other publishers in Japan may also have Manga contents with such toc of different order from reading order.

Although we will modify our EPUB files when we find to use such wrong order toc, I'd like to discuss the way to reconsider of this specification for reproducibility of printed books or I'd like to propose to change behavior of EPUBCheck to WARNING, or other messages, in order to keep availability of existing EPUB files.

As already reported mainly from Japan, errors by EPUBCheck will give critical impact because it will prevent from delivering EPUB files to eBook stores in Japan.

I appreciate if you have any interest this topic.