If your project has the Tickets tool installed, you will notice that the Milestones tab has been removed from your project's main navigation. You can now find it as a subtab in the Tickets tool.
A long time ago, we put Milestones on a separate tab because we were migrating users from Trac tickets, and Trac put Milestones on a separate tab. However, in reality, Milestones is always part of a Tickets tool. We removed the special case where adding and removing Tickets also adds and removes the Milestones tab. This will also reduce the amount of tabs in your project's navigation.
You can read more about Assembla's Ticket tool here.