This was the case in my case. I couldn't get the database removed, and than i found this.
Delete the mailboxdatabase:
Remove-MailboxDatabase databasename -Verbose
It then shows the reason why it can't be deleted.
In my case it was a systemmailbox that wasnt showing when i did
get-mailbox -database databasename
Now i could see what the reason was why the deletion stopped.
1. Start the Active Directory Users and Computers snap-in.
2. On the View menu, make sure that Advanced Features is selected.
3. Locate the Microsoft Exchange System Objects container.
4. Delete the SystemMailbox{yournumber} item.