My working theory: each language does modules in a different way. People think "Oh, a module system, I know this" and then run into issues when it works differently than their language. Just a theory though, I have not been able to validate it, or to figure out an explanation that works for all people.
And yes, more generally: as Rust continues to grow, more and more people will hit more and more edge cases, and they cannot always be fixed, thanks to being backwards compatible. That's just how things are as they grow up. More and more users also brings more and more use cases. It's a feedback loop.