For one thing, if you feel umcomfortable saying, don't say it. Could certainly be the Holy Spirit trying to convict you to stop. GOD will surely help you stop as well if you have a habit of saying that phrase, so pray on that.
On another hand, as Ghooost said it depends on what sense you use it. Say for example I just witnessed a car explosion before my eyes and I say it out of shock, I sincerely doubt that is in vain. On the other hand, if you say it so often in casual conversation (such as if your friend just told you something silly, like a joke) that could as well be in vain.
Let' take a look at what it means in "vain" anyway:
Vain
adj., vain·er, vain·est.
- Not yielding the desired outcome; fruitless: a vain attempt.
- Lacking substance or worth: vain talk.
- Excessively proud of one's appearance or accomplishments; conceited.
- Archaic. Foolish.
idiom:in vain
- To no avail; without success: Our labor was in vain.
- In an irreverent or disrespectful manner: took the Lord's name in vain.