In the opening scenes, Dennis McCaffrey is wearing an officer's helmet that reads "Engine 17". But, going to the fire, he climbs into the officer's seat on the ladder truck. If he was wearing the Engine 17 helmet, his place would have been on the actual engine. To ride the ladder truck, his helmet would have read "Truck 46".
In the apartment fire, Stephen goes in to save a little boy. When there's an explosion, Brian falls back and his boots are all the way up, on another shot when he's on the floor his boots are folded down.
In the final fire scene, both brothers are swimming in an elevator shaft filled with water, but as they are trying to escape that building moments later, there is no water running off them, or in their boots.
While Brian and Steven are talking on their dad's boat, there are several shots of a canal in the background. In most shots, it's empty, but in one shot, there's a barge afloat in it that abruptly vanishes.
When Brian McCaffrey climbs the ladder to the top of the chemical plant fire, the angle is so steep that he is required to use his arms to keep his balance. But, when he gets to the top, we see the angle of the ladder has been lowered.
When Rimgale has Brian lift the trash can to prove his theory on how the arsonist was creating backdrafts, Rimgale is smoking a cigarette. The cigarette repeatedly changes length becoming longer and shorter, and then longer again in each shot of Rimgale. There is no time for Rimgale to smoke a whole cigarette, then light another one and smoke most of another in this short scene.
The position of Brian's hands and arms when he is in the bar talking to the bartender right before Tim reads his station assignments. In one shot, they're holding the beer glass, in another shot, they're folded and in another shot, he's eating.
When Brian goes to talk to Ronald at the mental hospital, Brian lays out some reports and pictures on the table. Ronald picks up a report and starts to read while Brian asks him who's doing this. The top page of the report that Ronald has in his hands changes positions in between shots several times.
Several establishing shots of Co. 17 engines headed to fires early in the movie show them crossing a Chicago River bridge with Merchandise Mart in the background soon after leaving the firehouse indicating that Co. 17 is located near downtown Chicago. At the end of the movie when the pull back shots shows Co. 17's engines headed towards the fire, the skyline of downtown Chicago is considerably further away, indicating a location on the west edge of the city of Chicago
In the warehouse fire, when Bull is holding onto Axe and the explosion knocks them off the platform, you see Bull dangling from his "harness" and reaching for the beam in mid-air for a split second before the camera angle changes.
In the garment factory fire when Brian goes off searching for a person, there is a drain on the floor and you can see the fuel the crew spread on the floor, the camera then cuts to a different angle and when it returns the fuel is on fire.
In the final factory fire scene when Kurt Russell is wounded on the catwalk, the two firefighters who trying to get to Kurt are covered by William Baldwin spraying and soaking them with the water hose. One guy is wearing a hat and as the two reach Kurt, he takes off his hat and his hair is completely dry (as if he just got out of his dressing room). Though the hat would cover his hair from the water, he would still be sweating profusely due to the intense heat and wearing a heavy firefighters jacket.
The goof items below may give away important plot points.
In the opening scene, Dennis McCaffrey is verbally referred to as "Captain" a number of times. However, while responding to the fire in which he is killed, he is shown wearing the lapel pin of a Lieutenant (Single Bugle on red background) instead of the lapel pin of a Captain (Double, Parallel Bugles on red background).
When Bull is in the back of the ambulance and he starts crashing, the paramedics give him lidocaine to settle his heart rhythm. Lidocaine isn't given in severe trauma patients, because one of the side effects is hypotension, something he already has from the blood loss.