Alice is wearing boxers. The Reveal is that Alice is becoming Albert, or alternately, that Alice was/is Albert. (depending on what direction he or she is transitioning, either wearing the boxers as a step toward more masculine dress/a secret, or alternately because they are the only underwear that conceal an externally male appearance under the skirt)
Brenda defeats Alice, then takes her shorts and starts wearing them herself as a trophy.
Seeing Catherine's mistake, Alice offers her a spare pair of shorts to complete the disguise.
Alice's teammate Charlotte steals the shorts back from Bob and gets them to Alice, who puts them on over her panties just in time for the game to start.
Alice continues fighting in Vapor Wear, but trying to protect her modesty puts her at a severe disadvantage until her teammate Charlotte arrives with a spare pair of shorts.
Alice's teammates complain about getting constantly flashed during every fight, so Alice agrees to wear a pair of shorts... which happen to be completely identical to her old panties.
Alice fights in a miniskirt without giving a single Panty Shot, thanks to highly reliable usage of Magic Skirt. But when she starts to wear shorts underneath there's no more need for the Magic Skirt, and the audience gets to see her shorts all the time.
Zig Zagged: A team of miniskirted heroines are all participating in a fighting tournament on live television, so Alice protects her modesty by wearing shorts instead of panties under her skirt. Beatrice sees her first match and suddenly realizes that because she didn't wear shorts, there's no way she can fight without flashing her panties to the camera. So Alice takes off her shorts and gives them to Beatrice, who puts them on over her panties right before her round starts. But Alice's shorts don't quite fit Brenda, and halfway through the match they split wide open and Beatrice ends up flashing her panties after all. Afterwards, Alice comforts Beatrice and says she'll just use the spare pair of shorts she brought just in case. They hurry to the locker room and discover that the villainous Catherine saw the whole thing and stole Alice's spare shorts, in the hopes of forcing her to forfeit the match. Just then Alice notices a pair of shorts in another locker, and realizes that Dorothy must have forgotten to change into them before her match. They both rush back to warn her, only to see that Dorothy is already in the ring and about to start fighting in her hot pink daisy-patternedg-string. But before she can embarrass herself, her opponent Eve opens the match with a flying kick and shows everyone that she forgot to put on not just her shorts, but her underwear too. Eve is disqualified for violating the tournament's dress code, and Dorothy later reveals that she didn't forget her shorts after all, but decided that a thong would distract the opponents better.
Alice wears perfectly normal panties under her skirt, resulting in a perfectly normal Panty Shot.
Alice is designed as a serious Action Girl and the writers don't want to have her end up as Ms. Fanservice, so when the plot calls for her to fight in a miniskirt they give her a chance to put shorts on underneath since it's more realistic than using Magic Skirt.
The localization team is trying to target a younger demographic and/or get past very strict Moral Guardians, but Alice's pantyshots are just too frequent and blatant to cut completely. So instead, they turn her panties into shorts.
Lampshaded: After Alice wins a tough fight with a spectacular high kick, her teammate Bob points out it's a good thing she's wearing shorts under her skirt or the whole scene might have been cut.
Invoked: Alice is a miniskirt-wearing Innocent Fanservice Girl who flashes her panties all the time. Her friend Beatrice disapproves, so while Alice is in the shower Beatrice replaces her panties with a pair of shorts.
Exploited: Alice is forced to wear a miniskirt for the fighting tournament and wisely decides to replace her usual skimpy thong with a pair of shorts, so while she's in the ring Bob sneaks into her locker room to steal her unattended panties.
Alice discovers that someone switched her panties for a pair of shorts while she was in the shower, but she decides she'd rather go commando than wear them.
Played For Laughs: After Bob gets caught taking a picture of the Student Council President's Hello Kitty panties, she declares that all the girls must wear shorts under their skirts from now on. Bob soon starts exhibiting withdrawal symptoms.