Arsenal were swept aside by the Premier League's runaway leaders as goals from Sergio Aguero, Vincent Kompany and David Silva earned Pep Guardiola his first trophy in English football.
But the Gunners felt Aguero pushed Shkodran Mustafi in the build-up to the opening goal, while Kompany was perhaps offside when he turned in an Ilkay Gundogan effort to double City's lead.
Wilshere was also caught by Fernandinho with the midfielder having previously been shown a yellow card, but the Brazilian escaped a red card.
"Hard to put into words my emotions about yesterday," Wilshere wrote on Twitter.
"City are a good team and deserved to win yesterday.
"A lot of people have had their say on us and we have to accept criticism when we lose.
Hard to put into words my emotions about yesterday. City are a good team and deserved to win yesterday. Alot of people have had thier say on us and we have to accept cristism when we loose. That being said i can't accept some of the decisions that went against us yesterday. … pic.twitter.com/JgdO9ptqCx— Jack Wilshere (@JackWilshere) February 26, 2018
"That being said I can't accept some of the decisions that went against us yesterday."