First off, I'd like to welcome you to subterfuge! This is one of my favorite games and I love it when knew people try it out.
Also, I have encountered the same bug in a previous game, too. As mentioned above, it is sometimes activated if a saboteur is launched at an opposing sub when it is within 10 minutes of landing at a base.
Sorry that it messed you up so badly. Usually I find that it is worse for the person sending the saboteur because normally you would have to wait for your sub to return all the way back to the base then send it back at, but since the specialist and all of your drillers were teleported immediately to your base you can send it out right away.
Zyxe? Now that is a name I haven't heard in a long time.