At 06:29- the hole in the truck's hood is too small to have been made by the battery passing through it.
When Simmons shows Coulson the "brain cells", they clearly lack axons/dendrites, which are branchings from the cell walls that make neurons easily identifiable. Brain cells normally use these branches to produce tiny electrical impulses. The cells shown look like red blood cells.
Hollywood cliche- At 39:57 Coulson's Asgardian scar is revealed to be a large and ragged mess. Wounds, and their resulting scars, caused by sharp weapons tend to be straight and narrow just like the weapons that caused them.
After examining a fried brain, Simmons says it's been hit by 2,000 mega Joules of electricity, and notes that is almost double the power of a lightning bolt. Albeit there is no real minimum or maximum power for a lightning bolt. All lightning bolts vary wildly in power so the concept of double the power of a lightning bolt makes no sense.
While the first victim's dead body is being examined on the S.H.I.E.L.D. plane, his eyes move in one shot.
There are a few major plot holes in this episode. Viruses can't do anything outside of a host (they're not alive, they just hold DNA), so it can't have been leaving a rust-like deposit on the Chitauri helmet. The cure for a virus is NOT an antiserum (despite what Simmons keeps saying), it's an anti-viral. And if they "have any infected cargo" as Agent Blake euphemistically says, the very LAST thing they will do is dump it randomly somewhere on Earth, because it could spread the infection. An infected organism that dies is almost always incinerated at high temperatures to ensure the infection is destroyed. But the biggest single plot hole is when Simmons jumps out of the Bus. The Bus seems to be loosely based on an upgraded version of the Boeing C-17 Globemaster transport aircraft, which can comfortably cruise at 830 km/h, or 530 mph. From when Simmons exits the plane until Ward exits it after her is exactly 20 seconds. During that time, the Bus would have traveled about 4.5 km, or just under 3 miles. She wouldn't be drifting along under its tail, she'd be lost,and there's simply no way Wade could have caught her in the air and saved her.
Simmons is standing at the edge of the open hangar after "trapping" Fitz in the lab. He's screaming for her not to jump and he's pulling as hard as he can on the door trying to get it open. After Simmons jumps, he hurries to the table and grabs the "ANTISERUM", and the delivery device he made. Then, without touching nothing else, he turns from the table and goes running through the now wide open lab door.