When the SUV explodes, it is stopped at a red light one lane away from the curb (for location safety) with brake lights on. Later shots of the wreckage had it parked at the curb and surveillance video established no one was inside at the time of the explosion to be pressing the brake pedal.
A patient's eyes are taped closed during surgery to prevent drying and corneal abrasions. If a patient dies during surgery, nothing is supposed to be touched after the death until the M.E. does an autopsy to confirm cause of death. If they were negligent about this aspect of her care it might explain why her eyes are open.
When the first victim is shot in the metro-station the killer walks past the victim on it's right side. When reviewed on the cc-tapes the killer passes him on the left side.
When Morgan is driving back to Federal Plaza, his government issued SUV is a GMC Yukon XL. But when he pulls up to the roadblock, his SUV is a Chevy Suburban.
Cell phone towers do not rely on satellite links.
The show opens with the subway shooter walking away with his right shoulder adjacent to the subway wall. When Hotch is reviewing the surveillance tape, the shooter is walking away with his left shoulder next to the subway wall.
At the end, Derek tells Hotchner that he wants to annoy him for the next 3 hours. Both agents would be well aware that from New York to Quantico would be a minimum of a 5-hour drive.