I learned Japanese mostly through anime. Then when I was interpreting for my classmates and a Japanese transfer student, she ended up laughing for at least a full minute when I said "omae". Then the girls in the class started laughing as well, even though they didn't even know what happened. It was a bit embarrassing.
In anime you usually see younger people interacting whith eachother, so obviously they use a different kind of language. Actually, even that is probably different from what real teenagers would use in those situations. I believe in anime how they speak is also about showing their character, since there's so many ways to express the same things. (That's why the spiky-haired protagonist would say "Oi, koko da." but the shy underclassman wouldn't.)
We had an orientation at the Japanese embassy two weeks ago and we had a chance to speak with the ambassador, as well as some other Japanese people who work there. They were really friendly, but I was a little worried that I might say something rude or strange.
Also, I think learning from movies, games etc. is more of a passive thing, instead of a deliberate decision. I picked up both English and Japanese this way, without thinking too much about it. After a while I just noticed that I can understand stuff. And even though at the end of grade school I spoke English much better than German (which I had been learning for 5 years then) I didn't understand why I said things the way I did until I learned grammar in high school. And trust me, Japanese is more about understanding than memorizing, at least if you think about learning seriously.
Not to mention that it's a slow process, I've been watching anime for probably 5-6 years now, complemented with reading wikipedia, random free stuff on the internet, and a really basic book in library, and... well, I do feel somewhat confident with my Japanese, but I still think there's a lot to learn, mostly vocabulary-wise. Plus there's the kanji - anime won't help there one bit. Of course that's only my experience but my talent/skill to learn foreign languages is probalby a little higher than average.
Oh, actually I attended the intermediate Japanese lessons at University for about 3 months, and here's a few things that were new for me:
the difference between imasu and arimasu; some basic words, inlcuding a few colors, vegetables, fruits, furniture; most of the counting words