Before I start, let me say I know that tax questions can only be authoritatively answered by tax professionals, yada yada yada. but before i go through the trouble i want to make sure i'm not asking a dumb question (which i probably am!)

I recently opened a Roth IRA with Vanguard. Since I did this before April 17, 2012, I'm still able to contribute $5000 for 2011. When I opened the account, I was also given the option of making a contribution for 2012 as well. I decided to put in $5000 for 2012. It turns out that Vanguard put all $10000 into my account at once. Did I just make an excess contribution to my IRA? Or am I ok, because $5000 was designated for 2011 and $5000 was designated for 2012?

As long as $5,000 was designated for 2011 and $5,000 designated for 2012, you are fine. I'm 99.9% sure Vanguard's system will prevent you from making excess contributions (at least by asking you repeatedly "are you sure"). I use them and once tried to put in $50,000 rather than $5,000 by mistake, and it wouldn't let me.

Don't worry. You're fine. Just don't make additional contributions this year. I myself prefer to dollar-cost average a bit throughout the year, but to each his/her own.