i don't know if it was corrected in 1.0.4 but in the mermaid city if you got where the mermaid with the sea shell quest the will be a duplicated of the rare sea shell for the second quest. where the sea shell is in the dive section in the farm. (if you got the sea shell the duplicate diseapear so they are link)
In the glich that are still in 1.0.4 if you use jaguar to got on top of the forest of begining but use it on the right side you will jumo in the wall and will be stuck unless you have a jump feather.
In the south westhern plain one of the cave area have no collision on the top
one of the vine in the western plain is not place correctly so if feel off to see
in the snow city one of the door to the see the tp place is not set correctly to spawn to the left of the door.
Also i don't know if it a glich but i don't know if the secret room where you use the mystery key is suppose to be only accesible in new game plus because when i got there with my game that was in normal without new game plus the lever to enter the room was not there.