Well, thankfully these traces are on the outside layer so I will cut them for a temporary fix.
Thanks making things clear for me!

Hi! I have made the mistake of designing a PCB where mostly io 6 but io 11 is used. Today I discovered that my code crashes for obvious reasons and after looking at the datasheet: Pins CMD/IO11 and CLK/IO6 are used for connecting the embedded flash, and are not recommended for other uses. Does that ...