It seems they fixed that today:
"This patch fixes the Scuttle ship bug and a couple others. Do not use Scuttle until this goes live.
Differences between 1.2.67.0 and 1.2.69.0 include:
* If you Scuttled a ship, it was entirely possible for the wrong ship to be removed. Fixed that.
* If the Login server goes down for some reason, it's supposed to recover quietly - only the few people at a certain point in the login process should notice. However, we had introduced a bug that would kick everyone back to the login screen which you'd probably notice. Fixed that.
* It was possible for a nation to put 4 ports into contention at once. The limit is supposed to be 3. Fixed that.
* When someone of another nation chats in Area chat, you'd see "area_chat_event_empty" or the like, even if you had Diplomacy. Fixed that.
* Pirates were unable to have both Cut Lines and Wolf Pack in their toolbar at the same time. Wolf Pack would replace Cut Lines even though they're different skills. Fixed that."
Full information can be found here.