Plot hole: When Wilson does an ultrasound to check for cancer in Alex' ovaries he fails to notice the fact that she doesn't have a uterus. If he mistook her bladder for her uterus, which sometimes happens, she would have appeared to be missing her bladder instead. Yet Wilson doesn't pick up on anything being missing.
Plot hole: In the scene with Mikey in the NICU, the alarms start to go off, stating that he is in distress. The nurse screams "He's in V-fib!" and everyone rushes around him. In the next shot they show the heart monitor just before Chase shocks Mikey's heart. The problem is that the heart rate is so fast with one wide complex that it would actually be Supraventricular Tachycardia with 1 Premature Ventricular Contraction (SVT with 1 PVC), which is far less serious than V-fib and wouldn't require the heart to be shocked.
Answer: She would have No Reason to know it belonged to the CIA. If she did know he went off in the helicopter, all she would know is that it wasn't an ambulance helicopter.
Greg Dwyer