Hoppers Remove Bottles From Brewing Stands Immediately After They Are Put In

I was testing the duration of the new blaze powder mechanic for brewing stands in snapshot 15w42a.
I had made a hopper contraption to import and export water bottles through the brewing stand, when I noticed that my chest of water bottles that I had connected to my contraption was emptying incredibly fast.
I opened the brewing stand and placed a water bottle inside. The water bottle was sucked up by the hopper almost immediately, not giving a chance for it to brew.

How am I supposed to make my potions and become a Minecraft drug lord without my automatic brewing stand contraption?