I have encountered this issue actually also at the very beginning of E5L1, affecting the trashcan on the right (sprite #513). It's placed right on top of the shadow of the wooden crate. It doesn't cause any trouble in the original map, but in your patched version, you need to get really close to be able to shoot it.
*EDIT*
Your corrections also screwed up some texture alignment in the E5L1 bar area. Didn't exist before.
