A surprisingly good Time article outlines why one should be "suspicious" of Iran's election.
A few of the major reasons:
1) Consistent results across districts. This is highly unlikely actually true, given that Mousavi polled much better in cities (with what little polling there was), and Ahmedinejad better in rural areas. The demographics and voter issues are very different. Consistency across districts likely means someone pulled some numbers out of the air and threw them down.
2) Ahmedinejad won in every major city. Also unlikely. Some cities are particularly wealthy, young, educated, and were all but painted green the week before the election.
3) Ahmedinejad beat Mousavi in his own home town. This is just absurd. Mousavi was almost certainly most popular in his own district, and it is simply unbelievable that he could not win it.
4) Karoubi got less than 1% of the vote. This would suggest that many of Karoubi's personal campaign volunteers bailed on him at the polls.
The fact that Ahmedinejad beat Mousavi by approximately the same margin in every district, city or rural, and in Mousavi's home town are so statistically improbable that those that care about empirics cannot accept it. This election was rigged; I am officially calling it fraud.
Frankly, this is bad election rigging. Ahmedinejad had a serious popularity base, and as a friend said, "he could have gotten over 50% of the vote if the Ministry had bothered to count the votes." And, frankly, it is surprising that these results are so poorly rigged. As another friend said, "I could do better than this with the 2005 results and a python shell."
But with such blatantly rigged results, why is the US not standing up and calling it rigged? Perhaps Obama/Clinton fear that overt attacks on the election could harden the shell of the conservatives in power of the Guardian Council, or otherwise provide firepower/motivation against a new election. The EU is being more overt about it, perhaps because they are not as hot a topic as the US, or perhaps because they tend to follow a bit of a more friendly-idealistic foreign policy. Who knows.
But the clearly-rigged nature of this election gives more credibility to the allegedly-leaked results (although Ahmedinejad getting third seems unlikely, too, given how much noise his own supporters made). Unfortunately, the Council will struggle to be able to say, "oh, wow, hey, we found the real results!" and just publish them--it would be an admitting of systematic, centralized fraud and fakery. More likely, if they capitulate, they will find a few folks in the Interior Ministry they don't like, sack/imprison/kill them, and say that there were "sufficient irregularities" to require a second election, push it through, and only then give Mousavi the win. But, we can certainly hope for that.