When Mini-me and Number 2 reach for the cookies there are clearly two cookies visible on the plate, yet when we see Mini-me eating he has only one cookie and there are none left on the plate.
When Dr. Evil first introduces Fat Bastard to Frau and Number 2, his trademark "ice blue" eyes are brown, as they remain through Dr. Evil drinking a sip of Austin's mojo.
Mini-Me's cookie has more bites taken out of it alternately throughout shots as he fights with Scott to get it.
When Austin is knocking over stuff in the warehouse with his new car, the white barrels on the right and the screens in the back are standing up after they have been knocked over.
When Felicity is hammering the tennis racket into Austin's "shadow", it is almost up to the strings when the camera moves to the guards outside the tent. When the camera turns back to the shadow, it is only "in" up to the middle of the handle.
In the darkroom, Austin makes 8X10's of the pictures he took earlier. However, the door is left open, so the light coming from outside would totally ruin the photos. Since the photos weren't washed, they would deteriorate much faster over time.
Austin says he caught "The Clapper" in the Dutch East Indies in November 1964. The Dutch East Indies had ceased to exist years before that date.
Mini Me is described as being 1/8th Dr. Evil's size, but taking Dr. Evil's height (67 inches) and dividing by 8 would make Mini Me 8.38 inches tall. On the other side, taking Mini Me's actual height (32 inches) and multiply by 8 would mean Dr. Evil would have to be 21.33 feet tall.
Austin Powers and Ivana Humpalot are seen playing a game of chess, unfortunately the chess board was incorrectly set up, so that the bottom-right square is black. The improper backwards set up, is obvious, especially when they lick and suck the chess pieces. During the chess game, Austin's pendant is seen to jump about, from take to take.
When Austin crashes through the window with Robin Spitz Swallows and Felicity gives him a ride away in her car you can clearly see a British Cab with a white license plate. The plates should be yellow at the back and white at the front.
Just before Burt Bacharach and Elvis Costello sing, the camera pans. You can clearly see the mountains of LA/California in the background, although the scene is set in London.
Earlier, Austin says, it was remarkable how England looked "in no way like southern California", ironically speaking. Showing Californian mountains in the background of London therefore is merely consistent.
During Austin Powers' time travel, his car enters the building only a few stories up. Austin never changes floors throughout his entire visit in the nightclub, yet when he and Robin Spitz Swallows crash through a window, they fall much more than just a few stories, as if they were falling off of a skyscraper. Given the over-the-top nature of this particular scene, this is probably deliberate.
Elvis Costello appears as an adult in a scene set in 1969, but he was only fifteen years old that year. However, both the good and bad sides have access to time travel, so the modern-day Costello probably came back in time to perform for Austin.
Since the series specializes in spoofing the real history of the "past" that they travel to, the 1969 President should be a caricature of Richard Nixon. Yet there is no clue that this is supposed to be Nixon. Fictional franchises regularly use "fictional presidents" and fictional versions of other politicians so as not to "date" the films.
In the Mustafa scene, a European "cow crossing" sign can be seen along the roadside. Since the filming location is in Southern California, this must be a gag.
In the opening credits, the pink swim cap on the swimmer Austin's left gets pulled down over her eyes as she comes up out of the water....and she is trying hard not to laugh.
When Mini Me draws the picture of Scott being hanged, you can see that the paper was drawn on beforehand, and his pen never touches the paper.
When Fat Bastard is in bed with Felicity Shagwell, he leans over to get some chicken. When he leans back over towards her, some Velcro is visible on the fat suit under his left nipple.
When Austin travels in to the past the first time and crashes the car onto the dance floor there are fluorescent tire tracks on the floor indicating to the dancers where the car is going to be.
When Mini Me draws the picture of Scott being hanged he is using one black marker. However the picture is colored with two colors: Black and Red.
While Heather Graham has Will Ferrell in a headlock on the edge of the cliff, a fly briefly lands on his nose.
When Austin goes back in time to save Felicity on the moon, he inputs his destination as "ten minutes ago." But when Austin is running down the stairs to get to the time portal the screen that shows the destination already has "ten minutes ago" on the screen, before Austin ever types it in.
When Dr. Evil and Mini-Me enter the time portal in 1999, Mini-Me is on Dr. Evil's right. But when they emerge in 1969, he is on Dr. Evil's left.
When Austin first time travels back to his London pad in 1969, the song "American Woman" by the Guess Who is played. That song wasn't released until the following year, 1970.
When "Fat Bastard" shows up and is talking about eating "Mini-Me", he sings "I want my baby back ribs" and references Chili's restaurant. Chili's restaurant was not founded until 1975.
Austin Powers: The Spy Who Shagged Me (1999) supposedly took place right after where Austin Powers: International Man of Mystery (1997) left off in 1997, yet all references to the present label the year as 1999.
In the London Underground, the British troops are carrying American rifles and not British SLRs of the period.
Woody Harrelson makes a cameo as his adult self in a 1969 scene, at which time he would have been eight years old. Even if he did use time travel, there's absolutely no way anyone in '69 would know him.
When Mini Me puts Mini Mr. Bigglesworth under the table, he is obviously handing the cat to a crew member under the table instead of just dropping him on the floor.
After Dr. Evil's chair spins out of control, you can hear a member of the crew laugh out loud in the background, just after Dr. Evil says "sick as a dog".
When Shagwell and Austin make a guard fall into lava when in the cell, the mat the actor falls on is visible for a single shot.
When Austin is trying to "flush" Mini-me from his pants on the moon base, he is reading a newspaper. The name of the paper indicates it is from London, however the back of the last page clearly shows a USA weather map.
All vehicles in the UK until 1973 had black number plates with white/silver letters and numbers.
As Mini-Me tried to kill Scott Evil by pressing the red button on the control panel, Mini-Me's name already appears as one of the other four choices. About a minute ago, Dr. Evil didn't even know he had a miniature clone of himself, and this clone has not yet been named by anyone.
In the previous film, Number Two betrayed Dr. Evil and was incinerated. He obviously survived (much like Mustafa did; and judging from the burn on his face) but it is very unclear how and why he became faithful to Dr. Evil again. He didn't fully support Dr. Evil before his betrayal and Dr. Evil tried to kill him, hence this being one of the biggest plot holes between the two films.
If Basil and the Ministry of Defence knew all along that Vanessa was really a Fembot, why didn't they warn Austin? Seems illogical for them to keep it a secret from one of their top agents.
Numerous celebrities appear as themselves in the 1969 portion of the film but as their modern-day selves. While the good side had access to time travel, it makes little sense for the celebrities to travel back to 1969 themselves.
The President says that $100 billion doesn't even exist in 1969. In fact, total US federal government expenditures in 1969 amounted to $158.4 billion.
While singing his "Just the Two of Us" duet remix with Mini-Me, Dr. Evil states that Frau revealed Mini-Me's existence to him. However, Number Two introduces him for the first time in his Starbuck's lair.
When greeting Frau Farbissina, Dr. Evil asks, "Wie geht's es Ihnen?" which is supposed to mean literally "How is it going for you?" in formal German. However, he speaks redundantly, as "geht's" is a contraction of "geht es".
Ivana Humpalot calls Austin "Austin Powerovich". However, in Russian -ovich is the suffix for a patronymic (name of the father used as a middle name). Therefore, Austin's Russian-style name would be "Austin Nigelovich Powers".