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: 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.
The Healers - S2-E16
Plot hole: When Benton and Carter are having to do the surgery on Raoul in the ER after he was burned they are not wearing masks.Dr Greene had just said that the real cause of death in burn victims is infection and not the burns themselves.
Homeless for the Holidays - S3-E10
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: 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.
A Boy Falling Out of the Sky (a.k.a. Shifts Happen) - S9-E15
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.
Status Quo - S14-E11
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.
Answer: A man named Paul Sobriki comes into the ER in the season 6 episode 13 " All in the Family." He is complaining of headaches, Carter and Lucy decide to rule out meningitis and do a lumber puncture. Paul struggles during the procedure and believes that both doctors are stabbing him. Lucy, who is interested in Psych thinks something is wrong with their patient mentally, but Carter is dismissive of her. She gets cross with his attitude and she calls the psych department anyway to have a look at him. Later on and near the closing 20 minutes or so of the episode, all the staff start playing loud music and get a cake which appears to be blue lol, together to party as it's Valentines Day, Carter returns from somewhere and asks where Lucy is. He goes to check one of the rooms for her and Paul Sobriki comes up behind him in the dark and stabs him twice in the lower back, he collapses and as he falls unconscious he sees Lucy on the ground also. In the next episode, Be Still My Heart (ep 14), Dr Weaver discovers them and all of the staff work to try and save them, whilst Carter survives. Lucy's wounds are fatal and suffers a pulmonary embolism as Corday and Romano try to save her. Carter is grief stricken and feels guilty about the way he treated her, he becomes addicted to painkillers and Benton, Greene all help him and book him into rehab.