I mean some species are more prone to violence then others, they value private property diferently and soo on...
Does that mean that diferent species get treated differently in court?
Well, if the Federation is, well, a federation, then that presumably means that its various Member States retain their own systems of law and judiciaries within the larger Federation legal system. So exactly what one could be charged with would depend upon where one is.
Say, for instance, you're a Human Federation citizen living on Vulcan. If you wind up in a
koon-ut-kal-if-fee (fight to the death) with your best friend St'Even because the girl he's
pon farring over invoked Vulcan law to force you to fight on her behalf -- i.e., the Kirk/Spock situation in "Amok Time" -- and end up killing him in the fight, you probably wouldn't be charged with murder. On Vulcan, such a killing would be legal because of their species' biological and cultural traits. Federation law would probably justify it by arguing that anyone who consents to participate in a
koon-ut-kal-if-fee fight to the death has consented to their own potential homicide, and that therefore consensual homicide is legal if the local Member State's legal system allows for it.
That's just one example of Federation Member States potentially having differing legal traditions based upon biological and cultural history, of course. One could imagine others -- perhaps on Risa, there is no prohibition against adults and teenagers who have gone through puberty having sex, for instance, and thus the age of consent is much lower and applies universally rather than only applying to other teenagers, as is often the case in contemporary America. Perhaps on Bajor, the Bajoran religion is the established church, and there's no prohibition against mixing church and state in the UFP for Member worlds. Etc.