Plot hole: There are always family members right in the room while the doctors are literally cutting into the patients. The family is always creating a fuss or whatever, until someone asks for them to escorted out. A real hospital would never let family members into the room while they are cracking open their loved one's chest.
Plot hole: When Mark slips and falls in the staff lounge, he puts both hands on the table to catch himself - but we can see him (the actor) quite deliberately lower his head to one hand - this is supposedly where he cuts himself, but he actually hits his hand and not the table. This would not produce the deep cut he ended up with. Also, the head makes contact on the left of his forehead and he ends up with a cut on the right. And when we actually see the cut, it is vertical and logic tells us that it would have been impossible for him to have a vertical cut from the angle he fell.
Plot hole: During Season 5, the search for an ER Chief takes nearly a year and two nationwide searches, but is ultimately unsuccessful. At the beginning of Season 6, Romano is chosen as Chief of *Staff* in the blink of an eye, and Kerry is appointed as ER Chief just as quickly. Then, in Season 9, Kerry and Romano's positions are switched as though such things happen everyday. There's no way decisions of this magnitude would be made in such a brief amount of time.
Plot hole: Carol and Duncan escape out the back of the shop - but there are no police waiting for them, which makes no sense at all. In reality, with such a situation, the police would have been waiting at the back door. There seems to be no one around at all, as they were able to dash through an apartment. When they finally do run into a cop, he automatically assumes that Carol is an innocent bystander, and not one of the robbers. He couldn't have known this, and in reality, a policeman wouldn't assume it.
Plot hole: Jeannie is debating if her son needs an MRI or a CAT scan, She didn't want the CAT scan because of the iodine, they decided to give him the CAT scan and he immediately goes into the machine. He never got the Iodine and it would take about 10 minutes after the iodine before The Test starts.
Plot hole: Dr. Lewis is talking to a patient about pets, and how she is "banned from a pet store" because she isn't good with pets. She explains that the only pet she ever had was sea monkeys as a child. But, in the earlier seasons, she had a cat. We actually saw the cat at one point when her sister was staying with her and let the cat out of the apartment by accident.