I would guess, then, that this a coming feature?
/execute if fluid [X] [Y] [Z] minecraft:flowing_water/execute if fluid [X] [Y] [Z] minecraft:flowing_water(I greatly appreciate the changes Mojang has made to the command block system, by the way. It is so much more efficient and concise.)
I've tested and verified that this issue doesn't occur when a command block chain removes its own power. The issue has to do with one command block chain influencing another (where a command block chain is defined as any number of connected chain command blocks, and the impulse or repeating command block that "chain" powers them, for lack of a better word).