When the fighter jet is taxiing before take off it's an F18 but when it takes off it is an F15. Then when being filmed in the air it's an F18 again
Shortly after the beginning of the movie, when the two men are scuba diving, we hear them talking to each other during their dive, but the breathing apparatus' that they are using make it impossible to speak underwater.
Colonel Caldwell is wearing Captain insignia.
The Skipper of the USS Santa Mira is wearing Lt. Commander (04) insignia. That is unheard of for a nuke sub to have a Lt. Commander as Skipper. That position is relegated to Commanders (05) and Captains (06).