Steps to reproduce 

I cloned a repository (having 2 submodules) and disabled the option Recurse submodules in the Advanced options before cloning. Then, selected one of the 2 submodules and clicked the Open option. After that, not only the selected submodule was cloned but also the other one, which was not my intention.

Expected behaviour

SourceTree would only clone the selected repo

Actual results

All the submodules got cloned