Factual error: Sheldon says the movie Gremlins "baffles" him in regards to the instructions being very clear."Don't feed the gremlins after midnight." However, this instruction is only for caring of a Mogwai, not gremlins (the gremlins are formed by Mogwais eating after midnight). Sheldon, of all characters, would not mistake Mogwais for Gremlins and he would know the exact wording of the instructions.
The Vengeance Formulation - S3-E9
Factual error: Sheldon's voice becomes squeaky when helium is pumped into his office. But if the room contained enough helium to make his voice squeaky just by breathing, Sheldon would actually be suffocating due to lack of oxygen, the lighter helium having displaced the heavier oxygen. You can do it with a balloon because you can breathe normal air between huffs, but if you're in a room full of helium, you won't last long before passing out and asphyxiating.
The Vengeance Formulation - S3-E9
Factual error: In order to get vengeance on Kripke, Sheldon mixes a solution of hydrogen peroxide, saturated potassium iodide and liquid soap, creating a large foam blob. This is easy to replicate, and what you will get (and look carefully, it is what Sheldon gets) is a huge, aerated foam mass consisting almost completely of bubbles. It is barely heavier than air, and if dropped from a ceiling as we see later in the episode it would float harmlessly about the place. Whatever it is that drops on Kripke and his visitors later, it isn't the foam mixture we see earlier - it looks like some sort of custard mix.
The Large Hadron Collision - S3-E15
Factual error: At the very end of the show, Leonard and Raj arrive at the hotel, which is supposed to be in Geneva, Switzerland, to visit CERN. If you look out the "hotel" window, it looks like they're half way up Matterhorn, but in Geneva there are no big/rocky mountains anywhere near the city itself.
The Adhesive Duck Deficiency - S3-E8
Factual error: Maybe I'm wrong but I've had the dislocated shoulder experience and shouldn't hers be in a sling at her side not across her front right to left? This just seems odd.
Suggested correction: That type of sling is the best for preventing movement of the shoulder joint. It is the proper one.
The Wheaton Recurrence - S3-E19
Factual error: Sheldon and the team are league bowling and have a match with Will Wheaton's team. They are bowling on lanes 2 and 3. In league bowling, you have to bowl on lanes that start with an odd number because the ball return is shared between those lanes. In league bowling, you take turns with each lane so that any differences in the lanes evens out, and this lane layout wouldn't allow that.