There are a number of reasons for this, and so I am not really sure which you are talking about. I think that the most likely answer here is that the controversy has to do with the Electoral College. The Electoral College is controversial because a candidate can (like Pres. Bush in 2000) be elected even if he does not win the popular vote.
Although this is very rare, it is possible for the system to work in this way. This causes controversy because it seems antidemocratic, even though it is perfectly legal.
Please follow the link for more details about the 2000 election.
The Electoral College does not allow voters to directly elect the president of the U.S. Each state has electors who actually elect the president. These electors usually follow the voters within their respective states, but they are not bound to do so. The Electoral College was originally established by our founding fathers because they did not feel the people of the U.S. were qualified to directly elect the president. At that time, only the wealthy were educated, and newspapers were local rather than national. Electors would be chosen from the educated elite because they would know the candidates and issues better than the general population.Today, many people feel the Electoral College is outdated because we are more educated and have knowledge available to us through the various media.
In the 2000 election between George W. Bush and Al Gore, Gore won the popular vote, but Bush received more electoral votes. The election was decided in Florida where Bush's brother was governor. Many feel this election was unfairly decided and showed that the Electoral College is truly outdated.