It could be a couple of scenarios. Did you have any other Qtags inside the bags as well? The antenna that reads the chip inside the Qtag is underneath the belt you place the bag on.
The Qtag doesn't need to be visible on the outside of the bag in order for it to scan as the antenna can detect the chip within a certain proximity. Some people have a spare bag or backpack that has a Qtag attached within the main bag they're checking in which would cause the "multiple Qtags detected" error.
You could also see this error if one bag was on the belt & the second bag on the floor is too close to the belt so the antenna is detecting both chips.
I usually just stick with paper tags as that removes the need for anyone in the baggage makeup area to have a scanner in order to figure out where the bag is going.
Another reason to keep it simple is reduced hours for baggage services trained people who can trouble shoot missing bags so if anyone else is trying to find your bag a paper tag is easier as they mightn't know how to use or have access to a scanner.
I can't even begin to think what a mess it will be when the baggage handling is outsourced to contractors who have never worked in a fast paced domestic environment but that's a whole other story.