In 25 years of software dev, and most of that in developing user interfaces to things, I have never found a commonly repeated error that could be attributed to user error. It's always badly designed software that ignores the user's mental model that's developed based on using the software.

In this case, "git clone" clones a repo 99% of the time, because 99% of repos are shallow and simple. For "git clone" to only clone the top level when you have su modules instead of prompting to ask if you want a deep clone, or doing a deep clone by default because that's the expected behavior, is pretty poor design IMO.