It's raining in one scene but not in the next, several times throughout the movie (also pointed out by the director in the DVD commentary).
Beads on Marcus are different and shorter when they reach the shop than they were before.
When walking to the voodoo store, Marcus is not wearing his Marti-Grass beads. In the next scene, as they're leaving the voodoo store, the beads appear around his neck again.
Shawn takes the group to the tour on a bus which leaves the French Quarter in daylight. Enough time passes that the sun goes down, signifying they've been driving a while. Shawn then directs their attention to a passing cemetery which he claims is Saint Louis Cemetery #1 and which he says houses the tomb of Marie Laveau - except that cemetery is back in the French Quarter, just a couple of blocks' walk away from where the tour bus departed.
During the scene in the bus, it is obvious that the bus is in park (pointed out by the director in the commentary).
The door of Crowley house easily gets on fire. It would be almost impossible to light it with firecrackers. If you watch carefully, you can see that the boards below are wet from some liquid, probably a flammable one.
While Shapiro is running from Victor Crowley, one of the trees can be seen still in a planting pot.
When they are standing in front of the voodoo store, they refer to Bourbon Street as being behind them. When you are really at that store, Bourbon Street is in the direction they walk. You can see the bars on the corner.
When the older man get his leg bitten by an alligator as the tour boat is sinking, one of the girls makes the comment that with his blood in the water, the area will become an alligator feeding frenzy. However, alligators don't hunt by blood scent, as sharks do, so the man's blood in the water would make no difference.