When Phoenix finds the first clue, he writes the letter "D" in white ink/marker in the pop-up book. When he opens the book at the organ, the "D" is black.
In the barber scene, Paddington drops the houseplant when he picks up the phone. Later, the houseplant disappears.
After setting off the sprinklers in the barber shop, Paddington is seen wringing his hat out in the next scene, but he wasn't wearing it when the sprinklers went off.
At 37:50, when Knuckles takes a bite of Paddington's marmalade sandwich; the bite mark changes in between shots from the middle to the corner.
After the four escaping prisoners disembark from the hot air balloon, it should have quickly risen again due to lost weight.
The railway chase suffers from multiple errors: engine drivers have no control over where their train will go, even the most skilled of amateur drivers can't suddenly turn a family member into a burly stoker for a big hungry firebox, freight trains never commence their journey at platforms of London passenger termini, uncoupled vehicles will automatically brake to a halt, the couplings are American style instead of British, parallel tracks also have trains coming in the other direction, and buffers are very heavily built when a track ends next to a long drop into flowing water.
When Paddington calls the Browns from the payphone after escaping prison, he only dials six digits. London phone numbers have eight.
In the haircut scene smoke from a ceiling fan sets off every single sprinkler in a barber shop, it takes heat to activate a fire sprinkler not smoke.
In the prison canteen, Paddington reminds the Professor to always use a cake fork, while in Paddington 1 he is seen using his hands to eat the cake when having tea with Henry at the Paddington Station. Paddington has been living in London for a while, so he must have learned to use a fork.
When Phoenix pulls out the sword on the train, it clearly bends from side to side. Yet, the sword cuts through the stuffed animals without any problems.
Judy and Jonathan use a payphone to call Phoenix. In the 21st century they'd be much more likely to use mobiles.
When the BT telephone in the red phone box rings, it rings with an American (US) ring style. The phone rings with a long ring followed by a short pause then a long ring. In the U.K. the phone would have a double ring followed by a longer pause then a double ring. That all being said, the particular BT phone in the phone box wouldn't even ring with a bell, as heard in the film, but has an electronic ringer.
Judge Biggleswade bangs a gavel before hearing Paddington's case. British judges don't use gavels.
Throughout the series, the street next to Mr. Gruber's shop diverts to the left. However, when Paddington walks up to the shop just before he witnesses the robbery, the street diverts to the right.
The organ maker designed his secret mechanism to sound a discord if a wrong key is pressed, thus giving away its true nature and making the code easy to crack.
The second letter that Phoenix finds on the scavenger hunt is a "C", but when he is playing the notes on the organ to get to the treasure, the second letter he enters is "A" (he says "A" as he pushes the key). He should have played the "C" key.
Phoenix seems to fall for Henry's home inspection ruse far too easily. In reality, he would've expected some prior notification of an inspection, plus he shows no suspicion as to how the Browns got into his house in the first place, nor why they didn't attempt contact at the door like any other visitors.