Thunar sometimes transforms a folder to a file in Xubuntu 16.04, 16.10, 18.04 LTS, and 18.10

I have some scripts that creates folders by using mkdir:

...
mkdir bin
cd bin
mkdir make
...

It works perfectly most of the time. However, for unknown reasons, sometime, the just-created folders appear as a file in Thunar, a really annoying problem.

I can navigate into the newly made folder using the command line and the traditional cd, then run ls and other CLI commands.

Questions:

1. do you know what causes the problem?
2. do you know how to prevent it?
3. is it a Xubuntu issue or it is related to other Ubuntu dis?

OS details: The problem was observed in XUbuntu 16.04, 16.10, 18.04 LTS and finally in 18.10.