I couldn't be bothered to enter the museum in Miara Town, but instead went south. Found the Whirl Islands, got lost, then eventually found the Abyssal leader. After finishing her, everybody left. On my way back, I decided to check out the museum. There, she came to grab the bell in order to summon Lugia (which she already did) and told me to meet her in Whirl Islands (which I had already done).
Minor issue, but still off.