"I just think that despite whatever happened, there was a lot of things that I did and that we did as a team, and that number was special down there," Howard told the Sentinel. "And I was a little bit upset about that."
Harris, acquired by Orlando last season in a trade with the Milwaukee Bucks, wears No. 12 as a tribute to a close friend who died from leukemia as a teenager, according to the Sentinel.
It is unclear whether Howard knows why Harris wears the number. The Sentinel said Howard likely didn't know when he made the comment during the interview, which took place Tuesday.
Howard is entering his first season with the Houston Rockets following a disappointing one-year stint with the Los Angeles Lakers. The 27-year-old Howard addressed his controversial departure from Orlando, which traded the seven-time All-Star to Los Angeles in August 2012.
"There were some things that I missed about Orlando," Howard told the Sentinel. "There's a lot of situations that nobody really knows that I kept on the inside, but there's some things about Orlando that I missed.
"But I have no regrets. I'm happy everything happened the way it happened. Even though I got hurt in the process and I had to go through a tough time, it made me a better person. I'm more mature now. I know how to handle situations different than I did back then."
Howard bolted from Los Angeles after last season, signing a four-year deal worth $88 million to join the Rockets.
Howard acknowledged the widespread criticism he faced for leaving the Lakers but said he is at peace with his decision to sign with the Rockets.
"Everybody's saying I was a 'coward' for leaving [the Lakers], and I knew I was going to get that," Howard told the paper. "But I think with the situation I had to do what was best for Dwight.
"I know when I wanted to leave Orlando, and I decided to stay, I wasn't happy on the inside. I wanted to please everybody else and ended up hurting a lot of people by doing it the way I did. So, this time it's like I had a second chance."
The Rockets play the Magic in a preseason game Wednesday in Houston. Howard reiterated that he is looking forward to his future with the Rockets.
"I said, 'You know what? People are going to hate me for whatever reason, so I can't allow that to stop me from making my decision,'" he told the Sentinel. "I thought that my decision took a lot of guts because everybody's saying, 'How could you leave the Lakers and 6 billion fans?'
"But I don't care about being an outcast or about being somebody that may look bad. All I've got to do is win now, and I'm in the right situation."