The next time the person with more popular votes would lose the Electoral College was in 1876. By then all the States in the Union were casting popular votes. Democrat Samuel Tilden lost to Rutherford B. Hayes by one electoral vote. In this election, the electoral votes of Florida, Louisiana, and South Carolina were in question, both parties claimed victory in those States with electors ready to vote for each candidate. To determine which candidate received the votes, a commission was set up and just days before the March 4th inauguration the Compromise of 1877 took place giving Hayes the votes to win if he promised to remove federal troops from the South, thus ending Reconstruction.
12 years after that election, the outcome had the popular vote winner losing the presidency. President Grover Cleveland was defeated by Benjamin Harrison. Unlike 1876, there was no confusion just a clear victor in the popular vote and and Electoral College, just two different people. No problems like in '76 or in the next election with a similar outcome.
The country wouldn't experience an election like 1876 or 1888 again until the year 2000. But this election was more like 1876 and 1824 than 1888. This time one State, Florida brought about the chaos. The vote count in Florida was so close that Vice President Al Gore rescinded his concession because a recount was possible since it was so close. The Florida Supreme Court allowed the recounts, but the Bush campaign appealed to the United States Supreme Court which then stopped the recount, thus awarding the State's electoral votes to Bush.
Some pointless similarities...All the popular vote winners in 1824, 1876, 1888, and 2000 lost the Electoral College and were Democrats (Andrew Jackson would eventually go on to form the party by the next election). Jackson and Grover Cleveland ran four years after losing the Electoral College and defeated the incumbent presidents, Samuel Tilden and Al Gore never attempted a rematch. With the exception of 1876, all the Electoral College winners were ancestors of a president. 1824, John Quincy Adams' father was the 2nd president. 1888, Benjamin Harrison's grandfather was the 9th president. 2000, George W. Bush's father was the 41st president. Out of all the popular vote losers from those four elections, George W. Bush is the only one to win reelection, winning both the popular and the electoral votes in 2004.