When Jane have Molly in the water, at one point you see Molly waking up (camera is facing both characters). Then an over the shoulder shot to see our people on the bridge and Molly's face is towards Jane's back (facing the camera) and she is unconscious.
When the BAU and police catch up to the unsub as she's about to drown her latest victim, she's carrying her into a lake. The victim wakes up, and manages to escape, going deeper into the lake. The local police wade in and capture the unsub, and carry out the victim. As they're all climbing up the hill, the water in the lake behind them is perfectly calm. It should be quite agitated from having 4 moving bodies in it seconds before.
Onondaga Lake is one of the most polluted lakes in the world. It is unlikely that any sane (or insane) person would get in the water.
When Prentiss and Seaver are looking through Molly's diet log, she has recorded a 15-minute run at 5mph as burning 266 calories. In reality, Molly would have to weigh almost 300 pounds to expend that much energy during a short run.
There are several references to "Syracuse General" as a hospital. No such facility exits.