Hi I've already encountered this bug a few rc's ago and didn't find it in the bug tracker. Unfortunately I've never had enough time to look bit closer at it. There's a way to get some skills (like hide, better repair, speed etc...) twice or even from other classes. I think you don't really have these skills but they are shown in the skill-interface. If you have selected a skill in a earlier game, the same skill will be selected automatically later when you get enough points. Looks like there is missing a check if it's possible to have this special skill now or not. Could someone please have a look at this, get the necessary information (screens etc...), and make a bug report? I'm sorry, but I don't have much time at the moment, but I think it should be fixed in Empires 2.0.
Cosmetic bug only. You don't get the benefits of the skills, you just see them on the Skills interface. The devs know about it and I do believe it's been fixed in one of the new alpha versions.