In July 2017, Hernández filed an unsuccessful federal lawsuit against MLB, alleging that racial discrimination kept him from being promoted to crew chief and from umpiring future World Series games.

[7] He was retained for the 2000 season ahead of 13 of his National League colleagues, which the Philadelphia Inquirer termed one of the "surprises" of the 1999 purge.

[13] On April 8, 2019, Boston University published a study on 11 seasons of Major League Baseball data, almost 4 million pitches analyzed, to determine the accuracy of balls and strikes called.

[14] In 2020, after a dozen umpires elected to sit out the season as a result of the COVID-19 pandemic, Hernandez was made an interim crew chief.

[16] The Sporting News journalist Tom Gatto wrote in 2020 that Hernández "has earned a reputation for being one of MLB's worst umpires".

Andrew Mahoney, writing for The Boston Globe, reported that Hernández "has a reputation as one of baseball's worst umpires".

[24] On August 7, 2001, Hernández was the home plate umpire for a game between the Chicago Cubs and the Colorado Rockies at Wrigley Field.

A visibly angry Hernández was shown on camera glaring at McMichael from the field, muttering "son of a bitch."

It later emerged that crew chief Randy Marsh had ordered the ejection, threatening to stop the game unless McMichael was removed from the ballpark.

[3] In August 2017, Detroit Tigers second baseman Ian Kinsler was fined $10,000 by MLB for saying that Hernández was a bad umpire who "needs to find another job.

"[32] On October 8, 2018, Hernández was the first-base umpire for Game 3 of the 2018 American League Division Series between the Yankees and Red Sox.

"[34] Hernández declined to comment after the game, a blowout win for the Red Sox, but MLB issued a statement through a spokesperson: "There were several very close calls at first base tonight and we are glad that instant replay allowed the umpiring crew to achieve the proper result on all of them.

[17][35] Hernández did not hang up his phone when his interview ended, and instead continued listening to the subsequent questioning of another umpire that he knew was intended to be separate.

Joe Torre, MLB's chief baseball officer, wrote him: "Simply put, we find your asserted justifications for remaining on the line to be implausible, internally inconsistent, premised on facts that are incorrect and not credible.... we have concluded that you remained on the line in an effort to intentionally and deceptively eavesdrop on a confidential conversation in order to hear what [umpire] Hickox would say...

Hernández was also chastised for asking pitcher Homer Bailey for 11 autographed baseballs after Bailey's no-hitter, for making three incorrect calls that were later overturned on the basis of video replay in the first four innings of Game 3 of the 2018 ALDS, and for angrily throwing his headset during a different game when his call was overturned by replay.

[36] In July 2017, Hernández filed a federal lawsuit against MLB, alleging that racial discrimination led to his being overlooked for World Series games and crew chief promotions.

[38] Nearly a week after he filed the suit, Hernández was named to the 2017 All-Star Game;[39] he was also selected as first-base umpire for the 2017 and 2018 American League Division Series.

[3] Hernández does charity work for disabled children, including hosting a celebrity golf tournament every year.