In the previous season Michael sustained a gunshot to the chest - however, in the opening episode of the new season (set 6 months after the gunshot) there is not even a faint scar to be seen when he is wearing no shirt whilst in bed with Fiona.
Michael has cover as Russian FSB agent. When he is given a passport it is a passport of Republic of Serbia.
The grenades Michael uses to try to smoke Kessler out of the panic room are fragmentation grenades, not concussion grenades.
When Michael is directed to return to Washington DC from Miami, they show an airplane taking off presumably from MIA labeled with NWA, Northwest Airlines, and the pre-merger tail logo. The merger of Northwest and Delta was complete January 31, 2010.
When Michael is at the cantina speaking with Puente and Puente has his gun on him the CIA is giving Michael intel about the Russian operatives Puente would know - both first and last name. Michael says he spoke to Bannen, while Puente responds that he has, "never heard of Victor Bannen." How would he know his first name if he never heard of him?