After the prince exposes himself and Waters is confronting Lena about not informing him, the camera angle focuses on Lena while Waters is speaking. The timing of his voice and the movement of his jaw is off.
During one of the last battles, one of the SEALS mistakenly yells "Grenade!" when throwing an outgoing grenade. In reality, a soldier will yell "Frag out!" when referring to an outgoing grenade, while the term "Grenade!" is used to warn comrades of an incoming grenade.
During the first few minutes of the final battle, the lieutenant puts a new magazine into his gun and proceeds with the cliché "magazine smack" to make sure it's in the gun all the way. While attempting this, the lieutenant misses the magazine entirely.
When the Captain is standing on the carrier deck talking on the satellite phone, an F-18 Hornet traps (lands) on the deck behind him. 13 Seconds later, a second F-18 traps on the deck. It is not possible to reset the cable and clear the deck in 13 seconds, and would be considered unsafe to do so.
When the two fighter-bombers take off from the aircraft carrier in the final battle, they only have drop tanks, no missiles or other visible armaments. As they fly over to the battle, they now have six missiles each.
When the SEALs jump from the aircraft it is shown in different shots as two different aircraft types. A side shot shows a type with fins on the extremities of the horizontal stabilizer, but the shot looking up after they jump shows a conventional tail with a single central vertical stabilizer.
In the scenes following the discovery of the smoke bomb by the rebels, the first scene shows a line of men moving across the field, all of them holding their weapons in a left-handed position. The next scene, a closer one from behind the men, shows them all holding their weapons in a right-handed position. It is likely that the film of first scene was flipped so that both scenes show the men moving in the same direction - to the left of screen.
While Waters is talking to the doctor outside the hospital, the amount of sweat on his face keeps changing. Sometimes his face is dry, so he could have wiped it, but then the sweat comes back as it was before.
When Capt Rhodes sees Waters, he takes off his cap. His cap is still off when he yells and runs to Waters' men. But when he tries to help those three Seals and the camera changes, the cap is suddenly on.
The means of communications between Rhodes and Waters is not possible. Rhodes is using a satellite mobile phone whilst Water' unit is using a tactical radio with a satellite capability. It would also be inconceivable for a Navy Seal Captain to have to speak to his troops on a mission from the noisy flight deck of an enormous aircraft carrier with dedicated communication links set aside for those assets in the field.
During the scene where the group is traveling up the stream in the rain, the SEAL that carries the shotgun is seen with his M4 slung with the muzzle pointed up. Anyone with any weapons training would know to sling a weapon with the muzzle pointed towards the ground while it is raining.
At the beginning of the movie, when the SEAL team first arrives from another (unstated) mission, Tom Skeritt's character, a Navy captain (O-6), tells Bruce Willis' character to go see the "medic." A Navy man would always say "corpsman", not medic.
In one scene, the Captain of the USS HST is talking on a Radio to the SEALS while on the flight deck near the Landing Zone. As he's talking a E-2 Hawkeye is landing behind him. Although he is allowed in that area, he is not wearing a Cranial Helmet which is required during all Flight operations on any Aircraft Carrier. Even as the Skipper, he is not above the safety rules set in place during flight operations.
The planes providing air support are seen carrying two infrared air-to-air missiles (AIM-9M Sidewinders) and four radar-guided air-to-air missiles (AIM-120 AMRAAM) each, neither of which can be used against ground targets. Even if they could, the effect would not be significant against an enemy concentration of such size. The explosions in the movie look more like an incendiary weapon of some kind though, which is not what they were carrying.
When Willis and his team are exiting a Sea Hawk on CVN-75 (USS Harry S. Truman) at the beginning of the movie the carrier with which that chopper is assigned is clearly shown above the doorway as "USS Enterprise".
During the scene where Dr Kendricks was talking over the CB radio with a US embassy personnel for help, right after her first sentence, we hear the man on the other end reply. Yet, she never appeared to release the "talk" button, meaning she is still in "transmit" mode and won't be able to "receive" incoming broadcasts unless she releases the "talk" button first.
In the final battle when the SEALs are retreating to the Cameroon border, Navy SEALs would never get that separated from each other in that situation to the point where they would have to ask who is where and what their status was. Getting that far apart compromises all small unit tactics that SEALs are taught and the team would loose total combat effectiveness. Though they would still use air support, Navy SEALs would never make themselves that vulnerable.
On one occasion, the LT Waters refers to one of his men as "Sergeant," which is a rank that is not in the U.S. Navy. (This is not a "character error," per IMDb guidelines, as this is not an error that a SEAL or any Navy personnel would ever make in real life.)
Upon exiting the helicopter in the opening scene, one of the SEAL battle helmets falls off onto the deck and it's left there. As there are flight ops going on, that is considered FOD (Foreign Object Debris) and a danger to all aircraft air intakes. It would have immediately been picked up by a crewman on the deck.
Immediately after the initial extraction from the evacuation point that was 7.5 miles from the mission, the helicopters fly over the mission. If it was safe to fly over the mission at low altitude, then why wasn't the evacuation simply conducted at the mission itself? What possible benefit could accrue to the SEAL team or the evacuees by making them hike 7.5 miles through difficult and hostile terrain, for an evacuation about a day later than was possible?
Per U.S. law and military doctrine (e.g., Joint Publication 3-68), U.S. civilian citizens who are not employed by the U.S. Government cannot be forced to evacuate. When Dr. Kendricks refused, she should not have been forced to leave. When LT Waters reported that she did not want to leave, CAPT Rhodes would not have ordered him, even implicitly, to violate her wishes. (This is not a "character error," per IMDb guidelines, because it is a major plot point and there is no indication that CAPT Rhodes or the team is intentionally violating U.S. policy, or that their superiors are ordering them to violate U.S. policy.)
During the first helicopter extraction, there is a clear, flattened path through the grass straight to the helicopter, despite the fact that only Waters, Kendricks, and one other SEAL had walked through. This indicates the actors' movements to the helicopter through multiple scene takes.