I have a repo with many submodules
The git command sequence for checkout operation is missing a fundamental step.
1) git submodule deinit .
2) git checkout ...
3) git submodule update --init --recursive
Essentially the (2) and (3) are covered, but (1) is missing at all

Copy/Paste from SourceTree
"
git -c diff.mnemonicprefix=false -c core.quotepath=false checkout event-w-obj_ptr
Switched to branch 'event-w-obj_ptr'

git -c diff.mnemonicprefix=false -c core.quotepath=false submodule update --init --recursive
Completed successfully.
"

Pretend you are on master with 3 submodules: alpha, beta, gamma
Now checkout a commit that does not contain beta and gamma (could be a previous step in project development)
The result of not running (1) is that the 2 directories with beta and gamma are left on the file-system causing confusion!

This behaviour applies on branch switching too.

I'm not 100% sure 'cause I didn't test all possibilities, but I think you need to "git submodule deinit ." before any checkout operation.

This is a long standing issue affecting also previous versions