Cannot empty stacked bottled gases

Check the details tab on the bottle. If its 0.0 kg then you cant empty. Its not because they are stacked.

I think this bug tied to how building internal contents handled. When pump send last bits of its content into a pipe the information about this resource should be completely removed from pump data but instead its just set to zero which leads to appearance of this annoying zero mass bottles during deconstruction. Temporary workaround is save/load before deconstruction