This causes false warnings for users (and confusion for AbuseFilter maintainers, given T134678).
According to a comment, ContentTranslation's code:
Don't validate sections that are too short. The validations happen while editing is going on.
If I read it right, CT submits the text of a single section to the filters as if it were the content of the whole page! Obviously, this will cause false positives with filters which check for things in the whole page (e.g.: are there references in the page? [not in a specific section]).
This must be what causes the problem described by MisterSanderson on MediaWiki.org.