Plot hole: The FBI is looking for a "very tall" guy who has been identified as such by various witnesses and by their own expert due to the entry angle of a fatal bullet wound - 6'5" at least. They send Elena into a bar near the end of the show to meet the Albanian perp who when he arrives is barely average height.
Casualties - S2-E14
Plot hole: When Bradford and Chen arrive at her apartment to see the damage her newly adopted dog did, she discovers the dog ate her roommate's varsity jacket, but she had to turn the doorknob to open the door; there is no way the dog got into that room if the door was closed.
Mondays Are for Murder - S2-E13
Plot hole: In an effort to keep Glenn's death as quiet as possible, Higgins hires a private pathologist to do an autopsy to see if there were any foreign substances or poisons in his system when he died. A few scenes later it is revealed that Glen was undergoing chemotherapy. How is it possible that the pathologist missed the cancer and the chemo treatment in his investigation? What he found was an excess of antacids.