Was trying to make a water elevator that could be turned off and on when I came across this bug. I sucked up all the water except the bottom block with soul sand below it and the water column did not update, but the water source blocks went into the buckets. Water columns need to update when a dispenser interacts with them. 

After updating a block next to one of the bubble column blocks, every bubble column above the updated one will update and turn to air, but not the ones below.