System near applications seem to be not able to perform storage operations

One thing which came in to my mind today:
I flashed the last version of Fairphone Open (fp2-sibon-17.09.3-manual-userdebug.zip) via fastboot.

I remember that I was a bit confused about the file privileges (and ownership) of the unzipped files.
As I can see here:

there is nothing special todo before flashing. Even there is one reply which indicates that a chmod has to be performed in advanced before executing the flash*.sh.

I remember I did something like that as well, but I’m not sure if I changed the privileges of all files.
Could it be that the problems I described have something todo with a wrong privileges (and eventually also ownership) of the unzipped manual-userdebug.zip files and folders?