WyldStyle and Uni-Kitty are seen falling out of a spaceship with space clothes on, and upon their landing are cornered. The next time they are seen they are still cornered, only wearing their normal clothes.
When Emmet goes to buy overpriced coffee, Larry the Barista says, "That's 37 bucks." In the background, there's a woman in a Fabuland T-shirt next to the window. When Emmet replies, "Awesome!" she has moved a (Lego) meter forward and someone is opposite her.
After Bad Cop captures Emmet, he shows him footage of his friends talking about him. Emmet was captured in the evening, and when he escapes it's night, but the footage Bad Cop shows is in daylight. Since Bad Cop is only interested in Emmet because he has the Piece of Resistance (which he discovered only just before capture), there's no reason for Emmet's friends to have been interviewed previously.
The cannonballs stored on Metal Beard's back vary in number between shots, and they reappear briefly after he's fired them. At first, he fires all but two, then all are gone, then all the cannonballs reappear before disappearing again.
When Emmett and Wylstyle land in the Old West, Emmett asks what a Master Builder is, and the words "The Old West" are directly above them. During Emmett's asking or what a Master Builder is, the camera shot changes and the "The Old West" is way in the background.
In the Old West, Wyldstyle is riding a black horse and Emmitt is riding a brown horse. In the brief shot after Wyldstyle repeats herself by telling Emmitt there are other realms outside of Bricksburg, Wyldstyle can be seen riding a brown horse. She goes on to name all the other realms with brief shots of those, and when we return to our heroes, Wyldstyle is again on a black horse.
During Metal Beard's tale, the first time they show the Relic Room there is a gummy bear on the pillar between the floppy disc and golf ball, and there is a highlighter behind the golf ball between the key and pen cap. When they zoom in on the battery, it's sitting where the highlighter was and a bottle of white out is where the gummy bear was. (In scenes with Lord Business and Good Cop/Bad Cop, it consistently shows the white out and highlighter in those spots.)
Rainbows have have the longer wave lengths (Reds, Oranges) on the outside of the rainbow and the shorter wave lengths (Blues, Violets) on the inside of the rainbow. The rainbows in the movie are reversed with the Reds on the inside and the Blues on the outside.
When Benny and crew escape Lord Business' tower, the ship that breaks through the wall is made of only three small bricks before momentarily leaving the shot and returning as Benny's Spaceship and crew.
The goof items below may give away important plot points.
When President Business becomes Lord Business, his hair piece is removed and replaced with his helmet piece. However, when Emmet forces his way into his lair and knocks his helmet off, his hair piece is underneath.
Near the end when Wyldstyle is starting her TV speech, there is a guy in a white shirt with a brown beard/mustache who gets frozen by the Kragle, but a few shots later he is on the left unfrozen and moving.
When Ghost Vitruvius says "I know that sounds like a cat poster...", he dips down and the platform holding the string is clearly visible for a second. The digital release uses a zoomed cut to correct this mistake.
When The Man Upstairs is almost convinced that his son Finn is right, the camera focuses on just The Man while he's thinking. While some may mistake the flashing red dots on buildings to be the recording lights from the cameras, they are actually reflections of the flashing airplane beacons that are on the tops of several of the Lego skyscrapers in the basement. You can see the beacons in several other long shots of the set. This is not a goof but instead a rather clever detail.