I found some greater soul gems with petty souls in them, can you empty the gem?

No, just use them as magic weapon ammo, there is a gem you can use over and again, but better not to give spoiler, wait until you find it yourself.

Strange that they put those gems in the game then.. Atleast i think it was some big gems allready full of small souls..

It's random loot, makes sense as it can happens to you to if you kill low level enemies with an weapon with soultrap and only have larger gems.

might be a mod who clears them, tried to make on myself but it had some issues.