Don't blame yourself. The folks that relentlessly promote foundationless, also tend to dismiss the phenomenon you now have firsthand experience with. They claim the bees have unnatural prescience and will never over-commit to drones. I disagree: Unless you cull and grade foundationless, one can easily build an unsuitable brood nest with the results you document.
Sounds like you have recovered without losing the hive. Expect to see population drop as the current workers age out, however. Once placed in the honey storage position, that big cell makes great storage. Just mark the bars with a big "H" so the situation doesn't reoccur in the future.