Labyrinth of Refrain: Coven of Dusk is a weird game because events trigger story progression, but you can do them out of order, often times causing confusion. This is what makes the Three Towers of Umbra so confusing. The game won’t tell you explicitly what you need to do, since that is something of a spoiler, so you’re left with a pointless, talk to Madam Dronya message. Thankfully, your game isn’t glitched, you’re just missing a side task.
Towards the end of the level, when you’re in the third tower, you’ll encounter an event on the sixth floor. This event, pictured below, has you fight the Putrid Fly Queen. Depending on your build, formation and gear this might seem like one of those fights where you absolutely must return on a later date, but it can be won. In fact, you’re suppose to win it before you actually get to the top of the tower.
If you don’t complete it, the story will still progress, resulting in Alice changing, having to return to Furfur for a key, returning to the basement to explore the northern part and opening a door towards the top left, but it will be a dead end. By this I mean, you’ll be told to report things to Dronya and the objective will indicate you’re suppose to do that, though due to the story events going in a linear order, you need the second key from the Putrid Fly Queen to actually do that stuff.
For those having issues with the Queen, I strongly suggest trying to build around burst damage. Even if it costs you a lot of resources, the Queen isn’t terribly strong but can destroy a team if given the chance. For me, I put the Fairy Queen’s armor on my top magic user, infused her weapon with all legendary gear, used a series of buffs and debuffs and fire to maximize damage output. It wasn’t enough to make a joke of her but more than enough to win the fight with relative ease.