Hi @Lipetka
It seems that there were some errors in the pinout. As you pointed out, the RPIO06 pin was incorrectly assigned as Y17, thus being duplicated.
I have also received an email from Tim Frey indicating this issue and proposing a new pinout version with the correct pin for the RPIO06, U18. He also pointed out that the Arduino header pins SCL and SDA were switched.
Regarding the mismatching between the Raspberry Pi header pinout pins and the ones available in the reference manual. Tim Frey sent me a new version of the reference manual from TUL where the RPi header pins have been corrected, now being accordingly to the PYNQ Z2 schematics.
I leave here the updated version of the pinout. Thanks to @Lipetka and Tim Frey for the corrections.
PYNQ Z2 pinout v2.zip (3.1 MB)