Welcome in the forum, Severin.
Can you please post your complete project, so that we all can have a look at all of your settings. To do so, use
Creator->File->Create Workspace Bundle (minimal)
and attach the resulting file.
here it comes, the project in question is "USB-RIO-Hub" ! On the schematics, under the "Communications" tab, you will find a UART and an I2C (which work fine with the internal clock), as well as the SCB SPI that currently uses an external 8MHz clock. Switch it back to the internal clock and check whether it fails for you too. Thanks a lot for your help.