Minecraft 1.4.7, Snapshot 13w09c
Empty Glass Bottles stack to 64, but when placed in the output slots of brewing stands I beleive they are supposed to stack to one. However, it is possible to shift-click a stack of 64 glass bottles into a brewing stand. This also has the effect that a comparator reading the contents of a brewing stand expects the maximum stack of Glass bottles to be 64, not 1, outputting a lower signal strength than might be expected.
Also, using the new double-click to pick up a stack inventory feature can have some unexpected results. To reproduce:
1. Put a stack of nether wart in the input of a brewing stand.
2. Have a single nether wart in your inventory.
3. Double click the single nether wart. Notice you now have 64 nether wart, even though 65 total have dissapeared from the stand and your inventory.
This also appears to affect the output slots of brewing stands.
These bugs may be related to bug