Besides not being properly dressed for the clean room (no masks, gloves), there is a problem with the clean room. Clean rooms are overpressurized. The air pressure in the room is slightly greater than outside because it helps keep the dust out. You can't overpressurize a room if hanging plastic/vinyl slats acts as your door. And you need to pass through an air shower, after you are suited up, to enter a clean room. You open a door, walk in, the door closes, the shower starts and when it is finished the opposite door opens allowing entry to the clean room. Exiting happens in reverse. The 2 doors are never open at the same time. So, even if a dock door was left open, there is no possible way for a bird (or 2) to fly into a clean room.
In one of the episodes, Howard says that he and Leonard used to be best friends until Raj joined the group later. This is incorrect because in several other episodes, it is shown that Howard and Raj were best friends and Leonard joined the group later.