After some days trying to install several different Linux distributions I always got a missing file as answer from Grub when I tried to boot into the fresh installed system. I tried so many different things but nothing worked. I remembered that the Microserver could have some problems with large partitions. I installed a 8TB HDD and tried to use only one large partition for root and the installation never worked. It was also often mentioned that a boot flag must be setted but still nothing worked.
The solution for me was simple: Decrease the root partition to a small value or use a separate boot partition. I used a 200 GB root partition and a separate home partition with the rest of the space and everything worked with Debian.