It doesn't happen with every tower, but some towers lose their names. They still show up in the Waystone list as "<unnamed>", but when there are several of them it's hard to know where to go.

The Waystone can be deleted from the list and reactivated to get a new name... But if it's lost a name once, it's bound to do so again.

This is with version 1.3.5 on a server.