Random folders are considered apps
.app files have always been Applications for macOS. In reality, as you have seen, they are just a directory. If you right click and click "Show Package Contents" you will open the directory as a normal folder.

Most of the time the extension is hidden. This can be changed in File > Get Info >  Hide Extension.

I would suggest changing the extensions. If you prefer to keep the .app extensions you can change the a to a different Unicode character (that looks similar to an a). This will prevent it from being detected as an Application.