The mistake goes bigger than that. Since most of the third film (Ultimatum) takes place during the same timeline as the second (Supremacy).
The openning scene of Ultimatum shows Bourne running from Moscow police while he is injured. What is he doing there? How did he get injured? The obvious answer is that it takes place during the same time in Supremecy right after he was shot by the Russian agent hired to kill him (and ended up killing his girlfriend in India).
It isn't until the scene where Bourne tells the Joan Allen character that "You should get some sleep. You look tired." that the Ultimatum continues beyond where the Supremacy ended. That scene is repeated in both films. It is only at this point that the viewer realizes that most of Ultimatum consists of scenes and events that simply weren't revealed to us during Supremecy - but took place during the same time.