Multiple factors:
-Gordon dropped around 6-8 passes.
-Still getting acclimated to the Erhardt-Perkins system.
-Timing
-Brady technique/mental errors
-OL in flux
-Hammy
Should improve. We shall see..
According to pro-football-reference ...
Gordon's career average catch rate is 52%, on an average YPC of 17.3
In 2013, it was 54.7% on a YPC of 18.9
So far this season, PFR has him at 53% on a YPC of 18.3
Acclimating to the difference between the West Coast and the E-P , getting the timing down, Brady having more time to throw, Gordon getting into better game shape may all help a bit, but I'm not expecting a huge improvement in Gordon's catch rate if the Pats continue to use him the way they have been (mostly as a deep threat).
OTOH, Gordon's catch rate may improve once Gronk is back on the field (and healthy), and/or if Brady returns to distributing his targets more evenly (using Hogan, and even Dorsett, a bit more frequently).
Anyway ...
Cooks' catch rate last season was 57% on a YPC of 16.6 - the lowest catch rate of his career, by far.
In contrast, Hogan's catch rate in 2016 was 65.5% on a YPC of 17.9. That same season Gronk was 65.8% on a YPC of 21.6.
So far this season, Gronk has been 67.4% on a YPC of 15. - second only to Gordon in YPC.