The two questions can be used interchangeably to mean exactly the same thing, if you are wanting to know what is worrying a particular person whom you are addressing. In other words, you can either ask the person 'What's wrong with you'? or just 'What's wrong?' However, if you want to know what's wrong generally, e.g. with the weather/the atmosphere/a problem being experienced, etc. you would say, 'What's wrong?', whereas 'What's wrong with you?' would always be directed at a particular person.

Technically not, however the term "What's wrong with you?" is often used when someone does something offensive or behaves a certain way. A situation to use this in would be if someone harshly bumps into you on the street without apologizing. It's (often) an expression of your frustration/annoyance over someone else's actions. "What's wrong?" however indicates you're worrying about someone else, e.g. when they seem sad or stressed. This rule isn't absolute but it is vaguely what it comes down to (from my point of view, I'm no native Englidh speaker).

If someone is upset, 'what's the matter?' is better. 'What's wrong with you?' can mean 'Are you crazy?' or 'Are you stupid', so be careful with it. For something like your phone you can say 'What's wrong with it?' or 'What's the problem?' .. so, in the same way 'What's your problem?' can mean 'Does your brain not work?' or something! :)