Well it's the only season in his career bar maybe his last at Barca, where he didn't have the strongest side in the league.
I know you only said 'maybe' but this is what people mean when they say you use 'hindsight' too much.
Guardiola's last season at Barcelona was 11/12.
Barcelona added Cesc Fabregas and Alexis Sanchez to their squads, as well as moving Thiago up from the B team. They sold Bojan, Jeffrén, and Maxwell.
Real Madrid added Fabio Coentrao, Raphael Varane, Nuri Sahin, Jose Callejón, and Hamit Altintop to their squad, and moved on Pedro Leon, Sergio Canales, and Ezequiel Garay.
Neither Varane nor Sahin nor Altintop had any meaningful role that season, they played less than 1000 minutes each. Callejón only played 1300. So really the main addition was Fabio Coentrao.
You can't possibly tell me that the addition of Fabio Coentrao to Real Madrid not only offset the additions of Fabregas and Sanchez to Barcelona, but actually tipped the scales to Real Madrid's favor in terms of squad quality.
The only possible reason to think "Barcelona didn't have the strongest side" is "they didn't win the title."