The characters dived into water several times, yet many scenes after their dive into the water show their head hair completely dry when they should be wet.
After Scarlett heals the wound on Souxie's arm with the stone, Souxie's sleeve is left bloody and with big holes in it. When they've gone through the underwater tunnel and are approaching La Taupe, Souxie's sleeve is clean and there are no holes in it.
When George tells Benji he was in a jail in Turkey, you can see Scarlett walking behind him (11:30) however, she's shown in front of him again in the next cut.
Errors in geography
When they show the house of Flamel, they show that the house is on rue de Flamel, this is not true. Flamel's house is on 51 rue de Montmorency, rue de Flamel is only named after him.
The poem on Flamel's stone shouldn't rhyme in English.
The headlamps the characters wear are upside down. This was most likely done so the light didn't shine into the cameras.
In the catacombs all the main characters wear headlamp/camera combinations. The headlamps point upwards, yet the "footage" the are supposed to film is pointed downwards.
The headlamps used are all clearly on their lowest settings at all times. if they were at the highest or even "medium" settings, they would have illuminated the entirety of the confined spaces that the characters were in.
This was likely done to maintain some of "spookiness" that the film requires.