Something wrong with the tree's. Some of them you can walk right through and others not. Seems like a bug/mistake? The same applies to enemies.
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It is not a bug, it happens that the lower half of the tree has collision, while the other half at the top does not. This is to give a depth effect characteristic of top-down games.
You can easily change this by modifying the TileSet. Select the z-index option and change the values that are set in the tree to your preference.