Maybe a bit outdated, but incase some one still needs help here:
You need to configure the tileset in Tiled correctly, to the mentioned settings:
set to Hexagonal orientation, with 32 tile width, 28 height, and 16 side length. There's also an offset of 2 on the Y axis
Additionally the map need to have the same grid sizes and correct (flat top) orientation, so that the tiles don't overlap.