Late in the film it is shown that the window of Silky's suite in which the murder occurred is a couple of feet to the right of the corner of the hotel building, leaving no room for Silky's bedroom, which was shown to be to the left of the window (viewing from outside).
On Moran's hotel room door, there appears to be a deadbolt lock above the doorknob. However, there is no corresponding plate or bolt visible on the edge of the door - a shortcut set carpenters often make.
A vice squad raid on a supposed "Flower Shop" has a bunch of suspects filing out into a paddy wagon, but the open door reveals there's no roof inside, and the whole block is a false-front movie set. By WesternOne.
When Slip and Satch go out on the hotel ledge, the shadow of something (a crew member's head?) can be seen moving on the far right side in several shots.
The city street shown below Slip and Satch when they are on the hotel ledge is clearly not NYC footage. There are at least six vertical neon hotel signs on the far side of the street (the closest one says "LE ROYS"), and the one on their side of the street reads "BROOKS."