When Whistler shifts the van from reverse to drive, it makes the sound of gears grinding as if it were a manual transmission. An automatic transmission does not grind gears together, but the shifting motion clearly is that of an automatic.
After Bishop has described crossing a bridge, the shot switches to the van on a bridge. The first sound of a car going over a seam matches up with the van going over a seam, but for the rest of the shot, which includes the sound of several more seams, the van doesn't cross another seam.
While the guys are videotaping Janek working in his office he gets up to open the door to let Dr. Elena Rhyzkov in you can see the electronic keypad on the door. However no one notices it as later we see Bishop practicing picking a standard door lock, and when he arrives at the door the electronic lock is a surprise to everyone. Since they are able to zoom in on the keyboard when they are trying to get his password they could have zoomed in on the door to see the electronic keypad, and been prepared for it.
Not long after Carl (River Phoenix) enters the building asking if he can use the john, the security guard goes to look for him and, not seeing him inside the building, picks up a phone to report that the gardener is now missing. He aborts the call after seeing Mother (Dan Aykroyd) outside raking leaves, assuming he's the same gardener who went to the men's room. Immediately after the guard terminates his call, Mother says into his microphone, "OK, fellas. I'm outta here." The windows of the building are reflective so no one inside the building can be seen from the outside. Therefore, there was no way for Aykroyd to even see the guard inside much less know that he had stopped looking for the gardener.
Believing that he has located a hidden Martin Bishop, Wallace fires his pump-action shotgun into the ceiling four times, each time cycling the weapon to eject the spent shell casing and chamber a fresh shell. When Martin finally emerges and surrenders, Wallace cycles the weapon a fifth time without ever firing a fifth shell, thereby ejecting a perfectly good and usable round from the gun. While this may have been done intentionally in order to startle and intimidate Bishop, it also seems like a needless waste of ammunition.
When Bishop is marched into Cosmo's office at gunpoint, there are four light switches by the door, two of which are flipped up, two flipped down. However, when Cosmo leaves a moment later, they are all flipped up.
When the Sneakers are recording the conversation between Janek and Rishcov, Janek says he must finish his work, then there is a gap before Rishcov says she left a message. Playing it back later, the gap is significantly shorter.
When Elena Rhyzkow is trying to seduce Dr. Janek, she takes off her blouse. he first allows her to kiss him but then he refuses her. less than five seconds later, she tries to seduce him again and - takes off the blouse she already took off at the first attempt.
To circumvent the thermal security sensors, the temperature in Cosmo's office is raised to 98.6° F to match normal internal body temperature. Coming from a normal room temperature environment, Bishop's exposed skin would have been only about 91° to 94°, and his clothing even cooler, about 85° to 89°. This may have been enough of a difference to set off the alarm. The office should only have been warmed up to about 90°.
When Whistler is setting up the phone rerouting system to defeat the trace, the computer screen shows one of the cities listed as Durban, South Africa (an eastern coast city) but the actual location is clearly pointing to Cape Town, South Africa (a western coast city)
When the gang discovers that the circuit is the ultimate code breaker, and when Whistler has Carl enter different sites for them to connect to, Carl enters numbers on the keyboard's numeric keypad. Assuming standard Internet addressing nomenclature, and the fact that this movie is presumably set in the early 1990s, the numeric address would be IP4 formatted addresses: 4 octets with each number between 0-255. Carl doesn't enter anywhere near enough digits for actual routing to different sites across the Internet.
It is often asked how Bishop gets the answering machine into the office. He carries the backpack in his briefcase - this can be seen when he opens it in the engineer's office. The answering machine can be seen in the backpack.
Bishop goes to the trouble of defeating the voice entry system, which leads him to being caught. While Carl catches up with him via the access vents, getting into them needed a decoy gardener, and sending two people into the bathroom would have attracted attention.
The ceiling tiles that Martin and Carl use to move around above the floors in the Playtronics building are the hanging type, quite fragile like cardboard and would not be able to support an adult's full body weight.
In the limousine after Gregor finds out who Wallace works for tells Martin "You disappeared once before my friend. I suggest you do it again". But how could Gregor have known this? It seems doubtful that Martin would share such sensitive information with a potentially dangerous member of counterintelligence and not his closest associates. Creese even says to Liz that she was the only one who knew Martin's secret.
After Liz shoots the handgun and says, "I'm an excellent marksman! Woman," the gun has shot its last round and the clip is empty (the slide has locked back). If that were the case, the henchmen would surely have kept struggling.
The goof item below may give away important plot points.
Whistler immediately recognizes the "cocktail party" as geese babbling. But Martin was kidnapped after the evening concert and dumped the following morning, so it would have been dark when he was driven past the reservoir, and the geese would have been silent.