When using a dispenser with a bucket to remove a source block from a bubble column, it will remove the source block, but the bubble column still persists through the block that has falling water. Any subsequent uses of the dispenser will cause the dispenser to eject the bucket instead of trying to place or remove the water source block.

Since the bubble column is flowing through a block that is not a source block, I believe that the dispenser is unable to correctly compute that it can place the water in the empty source block and instead ejects the bucket.