Actually, no, the Electoral College has been a problem almost from the beginning. (And the only reason not from the very beginning, is that it was pretty much a given that Washington was going to be elected president unanimously, so there was nothing particularly contentious to cause problems.)
But the 1796 election gave us a president of one party and a vice-president of the opposite party. That wa distinctly uncomfortable. This introduced the practice of party tickets.
The election of 1800 resulted in a tie between Thomas Jefferson and Aaron Burr because the Democratic-Republican electors didn’t have the wit to ensure that Jefferson got at least one more vote than Burr, who was supposed to be running for Vice-President. This threw the election into the House of Representatives, where each state had one vote, the winning candidate needing a total of 9 of the 16 states to win. They voted 35 separate times, each time resulting each in 8 votes for Jefferson, 6 votes for Burr, with both the Maryland and Vermont delegations equally divided and unable to cast a vote for one or the other. Finally on the 36th ballot, lobbying by Alexander Hamilton, who hated both candidates, but feared Jefferson (with “wrong” principles) less than Burr (with no principles), the vote went 10-4 for Jefferson. This election resulted in the 12 Amendment to the Constitution.
The 1876 election was a mess thanks to competing slates from several Southern states, and no candidate having a clear majority in the EC. Finally, Southerners struck a backroom deal that they would throw their votes to Republican Rutherford B. Hayes (who had lost the popular vote to Samuel Tilden) if he would agree to withdraw Union troops from the Southern states still under their occupation and end Reconstruction.
Other elections won by the candidate who lost the popular vote:
1824 - Andrew Jackson lost to John Quincy Adams (I think that was another deal crafted in the House)
1888 - Grover Cleveland to Benjamin Harrison (Cleveland was the incumbant; he was elected to a second term by defeating Harrison in 1892)
2000 - Al Gore lost to George W. Bush
2016 - Hillary Clinton lost to Donald Trump
Five elections in total lost to the winner of the popular vote since the 12th Amendment “fixed” the Electoral College problem that resulted in two other very messy elections.
What else might you expect for an idea that came out of the Constitutional Convention’s Committee of Leftovers?