Never mind, fixed it myself, just had to change the layer value from 0 to -1. Are there values I should use or shouldn't use for custom textures?

How did you make these assets? Is it just an update in the spritesheet or did you make an entirely new asset?
Just by looking at the sceenshots, I'd say you might've either set it to the wrong layer or the origin is off. Check in the layer field in the properties toolbar if you accidentally changed the layer. If your sprite is exactly the same size, the asset has the same origin/position and xml as the one that is working, then it might actually be a bug.

It almost looks like you've added a bit of the tileset to the actual sprite edge, but it's hard to tell. Could you upload your xml and spritesheet somewhere so I could have a look? (if this didn't fix it)

Originally posted by StrikeUnleashed:

Never mind, fixed it myself, just had to change the layer value from 0 to -1. Are there values I should use or shouldn't use for custom textures?

Oh, okay great! A good tip is to look up similar kind of assets and try to use the same layers as they use. If you check the harbor doodads, their default layer is -60. The tileset for those assets, harbor.tileset, is set to layer -61. The harbor_base assets have a default layer -40, and the base.tileset is layer -50.

Thank you very much! :D