If you clone the project you will find, that these folders are in fact empty:
$ ls -la bin
total 0
drwxr-xr-x+ 2 fabiopoloni staff 68 8 Okt 12:18 .
drwxr-xr-x+ 8 fabiopoloni staff 272 8 Okt 12:18 ..
$ ls -la src
total 0
drwxr-xr-x+ 2 fabiopoloni staff 68 8 Okt 12:18 .
drwxr-xr-x+ 8 fabiopoloni staff 272 8 Okt 12:18 ..
There is also no .gitmodules
so it'll show you an error when viewing the status / syncing it:
$ git submodule status
No submodule mapping found in .gitmodules for path 'bin'
$ git submodule sync
No submodule mapping found in .gitmodules for path 'bin'
No submodule mapping found in .gitmodules for path 'src'
Since they're empty, the easiest way is to delete them and commit:
$ rm -rf bin
$ rm -rf src
$ git commit -a -m 'Removed empty submodules folders'
$ git push