何か違うんじゃない。
Nani ka chigau ‘n ja nai.
Something’s not quite right.

This is the sort of thing you might say to express doubt or dissatisfaction, to indicate that the situation has gotten mixed up or gone wrong somehow and all is not as it should be. The main part of the sentence, nani ka chigau (translated here as “something’s not right”) is conveniently vague; this expression is especially useful when it’s hard to pinpoint exactly what the problem is. It is often used in preference to more definitive statements such as:

それは間違っている。
Sore wa machigatte iru.
That’s wrong.

The preference for vagueness, which applies to many other types of expressions as well, seems to be based on a common aversion to the risk involved in making stronger statements—especially contrary ones. If you use the expression sore wa machigatte iru, for example, you run the risk of directly offending someone, and at the least you’re likely to be put on the spot and have to justify your objections in detail, when someone else replies:

それではお前はどう考えるんだ。Ⓜ
Sore de wa omae wa dō kangaeru n’ da.
Okay, then suppose you explain to us how you see the situation.

It is to avoid this very situation that people tend to stick to cracks like nani ka chigau n’ ja nai, which sound more impressionistic and don’t convey any strong message for which they might be held responsible. Suppose you encounter a couple out shopping, the woman trying to put together an outfit while the man looks on and tries to act helpful. You might hear the following exchange:

この色とこの色を組み合わせるのはどう？
Kono iro to kono iro o kumiawaseru no wa dō?
What do you think, does this color go with this other color?

う—ん、何か違うな。Ⓜ
Uun, nani ka chigau na.
Hmm, something’s not quite right about it.

The man, who isn’t very taken with the combination of colors, avoids the possibility of hurting the woman’s feelings (she might like the combination) while implicitly suggesting that she keep looking.

Another example: a photographer is trying valiantly to get a model to pose in a manner suitable for the picture he needs. He tells her what he wants and she tries one pose after another, but none of them is quite on the mark. Tacitly, what the photographer wants to say is, “You really don’t have any idea what I’m looking for here, do you?” Ever the diplomatic professional, though, he actually says:

どうも違うな。
Dōmo chigau na.
I don’t know, something’s not right.

　These days one often hears a different expression used, particularly by young women, to express essentially the same meaning as those above:

ちょっと変。
Chotto hen.
Kind of weird.

This expression conveys a strong sense that the objection is more subjective than objective and thus not necessarily explainable in logical terms.

– Source: A handbook of common Japanese phrases –