In 2016, Republicans won the White House and lost the popular vote by 2.1 points, or almost 3 million votes. In 2018, a similar story happened: Democratic candidates won the national gubernatorial popular vote by 3.1 points, or almost 3 million votes (again), but Republicans retained control of the governor's seat in a majority of states. How did this happen?
There would seem to be a pretty obvious answer. States with smaller, more rural and/or suburban populations tend to vote Republican, those with larger, more urban populations tend to vote Democratic: https://en.wikipedia.org/wiki/List_of_United_States_governors Thus one California or New York electing a Democrat more than outweighs Idaho, Utah, Wyoming, the Dakotas...
Another perhaps unappreciated factor is that partisan voters often aren't the ones who decide elections. It's the nonpartisan voters, who may make their choice based on factors other than party.
Project REDMAP and Donald John Trump, with a little help from the population of GOP-controlled states.
Project REDMAP was a Republican strategy towards political dominance by putting the vast majority of their resources towards winning governorships and state legislatures in the run up to 2011. when the redistricting maps would be drawn, allowing themselves to gerrymander these states to perpetuate Republican majorities for the next ten years. They needed both because while the state legislatures could propose the gerrymandering, the governor had veto power to block it.
The election of Donald Trump saw a record 15% of first-time voters that were motivated to go to the polls to support him. While they were there, quite a few voted for other Republicans. A record six governorships were won by members of the GOP in 2016.
Lastly, population density of the states in question. 15 of the 20 lowest-population states are majority GOP or swing states, which means that there are fewer overall votes for anything involving that state.
Because the national total popular vote means nothing! There is not a single office, election, issue, or anything that is decided by national total popular vote.
Governors are elected by voters in their own state. Same with state legislatures and US congressional representatives for each state. Those voters also elect the designated electors for Electoral College, and that elects the President. So there is no race that tallies base on "national vote".
It is only brought up as an "issue" by media when their chosen candidate is not picked. (have you ever heard of it when a Democrat wins the presidency?)