The Spaniard revealed his admiration for Arsenal's on-pitch display in their 2-0 win at Wembley, but he is far from pleased with how the club have acted off it.
City reportedly believe the Gunners are one of a number of clubs who called on the Court of Arbitration for Sport not to agree to delay their two-year European ban, which has since been overturned.
Guardiola is also understood to be frustrated with the way the north Londoners approached his former assistant Mikel Arteta before appointing him as head coach in December.
Speaking in the wake of Saturday’s game, Guardiola said: "The opponents always deserve my respect and credit, and Arsenal, they have it.
"I have all the respect for what Arsenal are on the pitch – not much off the pitch, but on the pitch a lot. So, I congratulate them and good luck against Chelsea in the final.
"Part of the good work Arsenal have done, I give them a lot of credit for – what they did, how good they defended.”