I've never once had Aetherflow fail to function. I think it falls into that "Itchy trigger finger" habit we tend to have. As one of an Arcanist/Scholar/Summoner's several abilities that does not obey a global cool down people tend to want to fire it off the very moment another spell has finished casting. Due to things like character animations vs recast time + small amounts of server delay you're often not ready to actually activate any ability.

If I need/want to use something like Aetherflow, Virus, Energy Drain, Bane, etc -- anything that doesn't follow a global cooldown I try to sneak it evenly between my usual recast times in an attempt to avoid disrupting my usual rotation as much as possible. It works especially well when finishing abilities that use cast times whereas I tend to catch myself tripping over my cooldowns when using multiple instant cast abilities that trigger a global cooldown (such as Bio, Miasma II, etc).

Just watch your timing & you should be fine.