Red mushrooms from the nether do not stack with red mushrooms from the overworld. Brown mushrooms stack normally.
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Actually, mushrooms depending on how you got them do not stack, for example, if you harvest say small red mushrooms from in caves and neither, these stack with one another, but if you harvest them from a large red mushroom they don't stack. The same goes for brown mushrooms, in that if you harvest them from the large tree like state they will not stack with its smaller counterpart.
Furthermore you can't 'quick move' them into an inventory containing like mushrooms, it shows an animation like its doing the move but it fails to the move (in some cases).
Actually, mushrooms depending on how you got them do not stack, for example, if you harvest say small red mushrooms from in caves and neither, these stack with one another, but if you harvest them from a large red mushroom they don't stack. The same goes for brown mushrooms, in that if you harvest them from the large tree like state they will not stack with its smaller counterpart.
Furthermore you can't 'quick move' them into an inventory containing like mushrooms, it shows an animation like its doing the move but it fails to the move (in some cases).
This was in early beta. It has since been corrected either directly or indirectly. They were all small mushrooms, some from caving and some from the nether. And they would not stack even if you drag and drop them. But now they do.