After the two scientists in hazard suits are dropped-off in Piedmont, there is a shot of the helicopter hovering overhead, yet the sound effect is that of a helicopter flying away. Moments later the helicopter does fly away slowly.
Boom mic reflection on level 1 red wall in conference room behind self destruct mechanism key insert. A minute later, boom shadow on wall behind actors as they discuss the odd man out theory. (:45 minutes in)
In the scene when the two scientists are first exploring the town, we see a shot of a priest lying dead on the steps of a church, eyes wide open. Right before the scene cuts, the supposedly dead priest stops his dead-eyed stare and looks to the right, obviously moving both eyes.
At the jet fighter crash site, a helicopter lands and one of its passengers vigorously slams two of its doors shut. This would never happen with experienced passengers. A helicopter's doors are light, fragile, and expensive. Thus one of the first rules of helicopter travel is to never slam the doors.
When the scientists get to the doctor's office in Piedmont, they leave the driver's side door of the van open, almost farther than a standard van door is allowed to open. When they return, it is open only that standard amount.
During the initial briefing on level 1, the overall display of the Wildfire complex shows the old man and the baby (2 yellow 'x's) as being on level 1. Dutton then asks Stone if they're both still alive, and Stone switches the display to a live video feed of the patients descending in the central core. On the wall behind the old man is a large "3", indicating he's passing level 3, but only 5 seconds have elapsed between the first shot and Dutton's question - not enough time for him to have gone from level 1 to level 3.
The plane approaching Piedmont for the initial flyover is an RF-4C, a two pilot reconnaissance aircraft. Later, a shot is looking forward showing the cockpit and forward section of the plane. It is clearly not a two cockpit aircraft nor does it have the distinctive profile of the F-4.
When they first subject the lab animals to the virus, on the right hand side of the screen in the reflection of the metal walls you can see the crew rushing towards the monkey cage to revive him right before they cut back to the shot of the scientists.
According to the map shown after the Situation Room scene, Wildfire was located in southern Clark County, Nevada, 46 miles from downtown Las Vegas, 34 miles from the Hoover Dam, and only five miles from Searchlight, Nevada (the smaller black dot below Wildfire); notably closer than 112 miles from any "...inhabited area..." as stated in the dialogue.
The screen showing the distribution of elements in the samples goes by atomic number, but skips over neon (10) for some reason. (It can't be because of lack of neon; other elements are indicated with a 0 or -.) The book does the same, in fact leaving out further noble gases (except helium), as if they were exempt from analysis.
The scene showing technicians troubleshooting a Teletype and missing a sliver of paper wedged between the machine's bell and clapper is unlikely. The bell in the type of machine depicted is located where such debris could not possibly fall onto it.
The captain who picks up Dr. Stone at his home wears no ribbons on his uniform. For this time period (the early 1970's), he should be wearing, as a minimum, the ribbon for the National Defense Service Medal, plus the Air Force Longevity Service ribbon.
The Air Force technical sergeant in Wildfire's communications room is wearing black or dark brown rank chevrons on his tan 1505 uniform shirt. In fact, the stripes should be silver-gray on a dark blue background.
In the scene where Major Manchek is at the jet's crash site, his uniform is incorrect. First, he is wearing a blue flight cap with his fatigue uniform instead of an olive green fatigue cap. Second, he wears no aircrew wings on his field jacket, even though he is wearing wings on his shirt earlier in the movie.
When the scientists are choosing filters to determine the size of the organism, the 1 and 2 micron filters are labeled "1M" and "2M". The scientific abbreviation for micron is "u" or the Greek letter "mu".
The helicopter that flies Stone and Hall from Vandenburg to Piedmont then back to Wildfire would have to fly over 1000 miles. The helicopter shown doesn't have nearly that range, not to mention remaining over Piedmont while Stone and Hall investigate.
On the Wildfire layout diagram, the baby and the old man are shown to be descending in elevators in the central core. When Dr. Hall later goes into the central core, there are no elevators in the indicated places.
At the beginning of the movie, vultures are shown circling over the town of Piedmont. Later, when the two scientists approach the town in a helicopter, the vultures are on the ground eating the flesh of the dead. The military even brought gas to kill off the vultures so they wouldn't fly off and spread the disease. What's interesting, is that no one gives a second thought as to why the vultures weren't dead. Even after they kill off a rat and monkey in the lab to test the disease no one wonders how it was that the vultures weren't affected.
When Dutton, Stone and Hall walk towards the electrostatic decontaminator, they are shown full-body from the rear to be nude entering the chamber. The next scene, tastefully blurred and solarized, still shows Dutton and Stone wearing athletic supporters, and Hall wearing bikini underwear.
James Olson goes under several decontamination procedures. During one early procedure, he has a very thick amount of body hair that looks like it is fake and applied. In a later procedure, the hair is much thinner and more natural. There is no explanation for the changes in hair thickness or texture.
The goof items below may give away important plot points.
Incorrectly regarded as goofs
The airborne contaminant kills almost everyone in the town, the laboratory animals, and the jet pilot in just seconds. When the capsule recovery team and later the scientist first enters Piedmont, there are live vultures flying over the town at night and later eating the corpses of the townspeople the next day. Dr. Stone is even concerned enough that the contamination is going to be spread, so they drop a double dose of gas canisters to kill the birds. They don't check the wind direction or have any concern that someone might still be alive in the town before they leave the helicopter to recover the capsule and do their investigations, because the gas is only toxic to animals with an unusually fast metabolism such as birds and does not harm mammals.
The characters state that the Andromeda Strain can only live within a narrow pH band: it affected those with a normal blood pH level, but not the old man and the baby who had abnormal blood pH levels. They go on to state that the virus from Piedmont will end up in the ocean where it will be destroyed by the ocean's pH level. This is plausible: healthy human blood maintains a pH of 7.35-7.45, completely outside the ocean's 7.5-8.4 range.
The story shows the only Destruct Substations located in passageways. Considering that individual labs seal off if they become contaminated, every single room should have had a Destruct Substation. If Dr. Hall had been stuck in the lab with Dr. Dutton, the story would have ended on a tragic note.