More than likely the bees just hadn’t sealed the gaps in the cells properly, it happens sometimes with new Flow frames. My suggestion is to drain that honey and use it for something else like cooking as it could be mostly nectar and high in water content. You should be right the next time round, if not then get back in contact as there may be some other issue with your Flow frames. After draining fully, pull them all out and inspect closely to ensure all the cells are lining up when in the closed position.
Lots of folks do it, and it is really a climatic decision, I personally don’t have an issue with it as some beekeepers swear by this method in our climate. For me, tried it and didn’t like it. Too much work and not a lot of honey. Sydney is split between the 2 brood box of SA and Victoria and the rest of the country, so many here just cannot decide and go for 2 as the default thinking it will swarm less. But even that is a myth. My colleague beekeepers who do go to 2 brood boxes all report the same thing in spring that the queen moves up to the top brood and leaves the bottom one empty where the bees begin to backfill with nectar and it never makes it up into the Flow frames. I’m with @JeffH on this one. This is from my personal experience, no harm in experimenting,