Nanyonjo, who took over the pageant in 2011, said that she is used to seeing a section of the public disagree with the official results.
She said they even always train the contenders on how to deal with negative feedback from the public.
"I'm used to this, it happens every year," Nanyonjo said in a media interview.
"You can't make Ugandans happy because they don't know what happens... they don't know what it takes, the process... to the finale. So, I'm used; it doesn't shake me.
She went on: "I just feel bad for the girls, especially when they are new to it. I get emotional sometimes... but we prep them..."
This year's public favourite was Whitney Martha Ademun, the sister of songstress Cinderella Sanyu Munyonjo, better known as Cindy.
Even Cindy herself believes her sister deserved to win.
"I saw that she should have won but I'm not an expert in that area... Maybe there are other things they looked at," Cindy said.
Ademun was the first runnerup.
Because of her association with singers likes like Eddy Kenzo, Spice Diana and Fik Fameica, some people believe that they may have influenced the decision of the judges.
Hannah Karema Tumukunde, who has repeatedly said she did her best – is not the first Miss Uganda to be rejected by the public.
They are always rejected for different reasons. For instance, for Tumukunde, people believe she is not eloquent.
Leah Kalanguka was rejected by the public in 2014 because she wasn't beautiful to the Miss Uganda standards.
When Phiona Bizzu was announced in 2012, there was booing and some walked out of the event. She was rejected on the same grounds as Kalanguka.
In 2010, Heyzme Nansubuga was also spurned and even Allan Kasujja, who was one of the judges, said she wasn't the judges' favourite.
Lillian Achom, who was Miss Uganda from 1997-2001, is the longest-serving Miss Uganda and she always faced backlash because the public saw her as the always-smiling girl who did nothing.
She participated in the contest while still a student at Makerere University after being dared by friends. Then won and found herself clueless.
Dr. Rehema Nakuya, who was a medical student, missed training camps but ended up winning. The public believed the then-organiser Sylvia Owori handpicked her to give credibility to the pageant. She was Miss Uganda in 2002.
Aysha Salma Nassanga, who was Miss Uganda 2003, was rejected because she was half Senegalese (father) and half Muganda (mother)
Betty Nantunga, Miss Uganda 1995, participated without her father's approval and when she won, he flew her to India for university. He even wanted to sue the pageant organisers.
Praise Akankwasa, Miss Uganda 2005, was handpicked because that year the contest didn’t go through the activities they normally do.
Oliver Nakakande, Miss Uganda, 2019, was bashed by the media so much that Uganda Communications Commission even banned a TV show, for attacking her physical attributes.
