At 00:30- The bus number is 539 but at 06:53 it's 1330.
When the team is at the bus following the explosion, the exterior of the bus appears to be in pristine condition, which is highly unlikely given the strength of the explosion.
When Spencer Reid is speed-reading 'Empty Planet' in Professor Kent's office while she watches, the actual book is the fantasy novel "Shadowed By Wings," by author Janine Cross.
The city buses in Seattle are called Metro or Sound Transit, not Seattle Municipal Transport.
When Morgan asks Garcia to look up domestic terrorist activity in the Seattle area, specifically anti-technology is shown blinking and highlighted in Garcia's screen before Morgan actually asks for it.
At 04:15- there is a fog generator between the two cars.
Agent Casey says the driver was one of the two people killed in the bus explosion since he was one of the closest to the blast. The explosion is obviously not at the front of the bus, but about a third of the way back. The driver was therefore not one of the closest seeing how many people were on the bus.
When Gideon is sitting in the SUV, talking with the unsub (at 22:10), the camera and cameraman can be seen in the reflection on the back of the side mirror.
You can see palm trees in the background when they are supposed to be in Seattle. Seattle doesn't have palm trees.
After the (arrogant) first guest speaker of the professor is killed by a bomb in his car and the professor tells Gideon that the second guest speaker is located "across town", the next thing we see is the team racing up the stairs to the parking lot instead of just calling the guest speaker to tell her of the situation and tell her not to get in her car.