They fixed that by making one scan only count for one mission, and needing a new instance to rescan.I bet they did it to "fix" the Quince trick where people took 20 missions to the same location and then scanned a dataport to finish all 20 at once. They're using a sledgehammer to kill an ant.
Personally, stacking is just a symptom of bad mission design. For a select few (i.e deliveries/ transportation and sourcing) it makes sense, but for most it doesn't.