The biggest issue I’ve seen is when companies hire 4 junior engineers with zero or minimal Rails experience to bootstrap their product, let them loose, and… yeah everything quickly becomes a mess.

Nobody understands the conventions so they cargo cult whatever they found from a blog that was last updated in 2013. Or they find novel and extraordinary solutions to problems that the framework literally already solved. Or they have zero experience modeling things in a database—much less doing it the way ActiveRecord encourages—so every battle is always uphill.

The biggest problem with convention over configuration is when you have a team where nobody understands the conventions. But what else do you expect?