Girona are City's Spanish club partners and count on loan players from the English giants.
Guardiola said: "They made a bad final part of the season in terms of results, because of the friendship that unites me with Eusebio, it's bad for me.
"The history of Girona has been more in Segunda than in Primera but football is wonderful.
"Quique Cárcel is one of the best. It's a shame, but that's the way it is."