Voting your conscience is not always right.

In short, conscience may not always be right. And one is not obliged to follow a sick or erroneous conscience. So the advice to follow one's conscience is deficient. It needs to be a well-formed and healthy conscience.

Examples of sick consciences are scrupulosity and laxity. The first feels guilt where there is no sin, the latter feels no guilt despite the sin. And if one has a sick conscience, then one needs to see a spiritual director for "treatment".

If one's conscience is healthy, then there is still a need to inform or educate it. The bishops issued guidelines in a document entitled "Forming Consciences for Faithful Citizenship: A Call to Political Responsibility from the Catholic Bishops of the United States" where it was stated:

34. Catholics often face difficult choices about how to vote. This is why it is so important to vote according to a well-formed conscience that perceives the proper relationship among moral goods. A Catholic cannot vote for a candidate who takes a position in favor of an intrinsic evil, such as abortion or racism, if the voter’s intent is to support that position. In such cases a Catholic would be guilty of formal cooperation in grave evil. At the same time, a voter should not use a candidate’s
opposition to an intrinsic evil to justify indifference or inattentiveness to other important moral issues involving human life and dignity.

42. As Catholics we are not single-issue voters. A candidate’s position on a single issue is not sufficient to guarantee a voter’s support. Yet a candidate’s position on a single issue that involves an intrinsic evil, such as support for legal abortion or the promotion of racism, may legitimately lead a voter to disqualify a candidate from receiving support.

These and others would have made it clear to any conscientious Catholic that a vote for Obama was immoral. However, others did not see it that way because they were mislead by fake Catholic groups who misrepresented the Catholic standards and by the politicians themselves who misrepresented their positions. Because of this, one has the duty to get down to the truth by looking at the candidate's voting records and past activities to confirm the veracity of his claims.

References:
1. http://www.ewtn.com/library/scriptur/conscien.txt
2. http://www.faithfulcitizenship.org/