Police wouldn't shake a hanky or cloth they think might be evidence. When Rizzoli picks up the hanky from the bushes, she shakes it as she picks it up, possibly discarding important forensic evidence.
Modern vehicles have small restrictors for unleaded fuel nozzles in their fuel fill necks that would not allow an item the size of a thick sock to pass through as Maura did in her experiment. Additionally, a thin cloth such as a handkerchief that would pass by a restrictor would not impair gasoline enough to shut down the engine. To do this, an item such as a plastic sheet would be needed, but that would float on the top of the fuel and never make it to the fuel pump pickup, which is located at the low point of the tank until the car was almost out of gas.
Maura cannot possibly know the murder weapon was metal regardless of the tests she runs, and certainly not by a simple visual examination of the body. Contrary to what they say in almost every police story, metal fragments are not left behind in wounds so she has no test to determine the object was metal.
Unless it's a deluge sprinkler system, the burning cigarette would have only tripped the sprinklers in the mens' room, not the entire basement. As there is sensitive equipment in the lab, there wouldn't be a deluge sprinkler in that area either.
The killer closes the hood on the car, finishes bludgeoning the victim, and walks away. Whatever was done to disable the car was not fixed so it should not have started when Jane turned the key.
"Wareham" is pronounced with one and a half syllables: "ware-um" with the second syllable slurred to have nearly no vowel sound. Detective Holiday has been with the Boston PD long enough to know how to pronounce local city names (especially as this pronunciation of the -ham ending is quite common in the area).
The "flair" on Dr. Isles's pink dress is called a peplum. Dr. Isles is a known connoisseur of fashion and should surely know this word. It's also quite surprising to see her in this expensive new dress in both the lab and the garage with no lab coat over it.