Hi Gerriko,
This problem exists only on Linux and is due to max limit of files that can be watched in the workspace. It is described here: Known issues and troubleshooting - Known issues and troubleshooting | Mbed Studio Documentation
Issue exists also in VSCode. You can find a solution here: Running Visual Studio Code on Linux
Unfortunately Mbed OS has a lot of files and limit is hit after 2 programs. It can however be easily increased.
Thanks,
Arek - Mbed Studio team