In Nichijou, Nano hits her toe in this manner, something the Professor (8 years old) solves by simply taking her toe off. And if you turn the big wind-up key in her back, her toe flies off like a rocket. Also, it has a USB port.
Although there were a few times where this happened to Tubby in the Little Lulu comics, a special mention of this trope comes up in episode 2 of the Little Lulu anime; Tubby, upset that Plan A in discouraging Lulu from her babysitting duties did not work, runs up to his room and kicks the dresser drawer in his room, a little bit too hard, which causes him to hop around in pain while holding one foot.
Detective Conan: Conan has had to improvise a few times on things to kick, so he's also hurt his foot as a result.
On the very first episode of the anime, Usagi's brother Shingo comes home to find her banging on the front door after getting kicked out of the house again. He then proceeds to make fun of her on his way inside, and when she tries to "Sailor V Kick" him in retaliation, he slams the door shut, causing her to kick the door full force and make a very funny face.
While attending at a traditional tea ceremony, Chibiusa and Usagi's feet fall asleep from assuming the wariza sitting posture for longer than they can bear. This elicits a few snickers from Usagi when she sees Chibiusa struggling to maintain her composure. Cue Chibiusa silently punching Usagi's feet from behind, sparking a war of back-and-forth foot-punching.
In the SuperS film, Usagi stomps the foot of an evil villainess who wanted to combat her with "a dance fight".
In Sailor Stars Nehellenia forces a barefoot, exhausted, freezing and depowered Usagi to walk through a staircase full of thorns to get to a brainwashed Mamoru. Beinga Plucky Girl, she does.
Dragonball GT: In the World Martial Arts Tournament, one of Goku's opponents kicks him when he's distracted. However, the power gap between them is so great, the poor dude may have well kicked an iron safe - he's soon seen crying and clutching his foot in agony afterwards, and Goku wins by default.
Giroro does this after being rendered clumsy by the loss of his trademark belt, which causes him to stub his toe on the door frame.
In a later episode, the platoon is inspired by Natsumi hitting her foot on the corner of a dresser, so they patent an army of dressers specially designed to hit peoples' feet as painfully as possible in order to distract all of Tokyo with pain, thus making them completely vulnerable to be conquered.
In Rave Master, Elie tries to carry Plue to a hospital, but injures her feet on the rocky ground and curses herself for forgetting to put her sandals on, because she took them off earlier from exhaustion. Haru catches up to them and wraps her feet with strips ripped from his shirt. In the anime, she is barefoot to begin with after changing into her clothes following a bath at the nearby hot springs, and skipped putting her boots back on. The scene is also toned down where she runs across the mountainous terrain (in the original, her feet were cut open and bleeding, but in the anime, they're just badly scraped up) The slightly unfaithful English dub lampshades this when Elie curses her hastiness:
(Japanese) Elie: (tiredly) Oh, I see... I ran in bare feet...
(English) Elie: (annoyedly) It would have taken two seconds to put on shoes, but no-oooo!
In Fairy Tail, King Faust punishes Coco by using a blast from his magic staff to burn her feet. She manages to run away, but eventually collapses from the pain and is carried by Lucy.
Erza Scarlet also injures her foot during the Grand Magic Games, after pushing Kagura out of the way of some falling rubble; which then falls onto her foot. This injury proves consequential to Erza, for the remainder of the games and the dragon battle that follows.
One Piece: At one point during Nami's fight against Ms. Doublefinger, the latter charges at her enemy with her hair turned into spikes. Nami manages to protect herself, but one of the spikes pierces right through her foot. Nami, though obviously in pain, shrugs it off, as it is nothing compared to what Vivi is going through, and pulls her foot away.
Sanji suffered this in spades during the second movie, Clockwork Island Adventure, while squaring off against Boo Jack's spikes, because his shoes were on board the Going Merry when it got hijacked (the crew was at a beach and forced to go to a wedding shop for replacement clothes) and he was stuck fighting in a pair on unsatisfactory sandals that did nothing to protect his feet and were subsequently lost in combat. When he finally got his shoes back in their rematch, it quickly turned into a Curb-Stomp Battle in his favor, and he even broke Boo Jack's spikes with each kick!
Luffy, in general, is the victim of this trope on and off because he won't wear proper shoes, even in a frostbite-inducing blizzard. In Heart of Gold, Luffy accidentally steps into a pool of stomach acid while inside a giant angler fish. Since he is militant about wearing nothing but sandals, he suffers the drawbacks here.
In One Piece Film: Gold, one of Gild Tesoro's lackeys steps on a roiling casino coin that Baccarat tossed out into the battlefield, breaking his ankle. Baccarat's powers render her a literal Karma Houdini who steals luck from other people by touch, and he was one of the unlucky ones, pun intended. As a result, he stumbles and causes a chain reaction that eventually doubles back on Usopp, Chopper, and Brook. Then, just to twist the knife, the casino coin magically finds its way back to Baccarat.
Bleach: During the final battle between Ichigo and Byakuya in the Soul Society arc, while they are clashing with their blades, Byakuya takes one of his other thousands swords and stabs on Ichigo's foot, so he cannot escape immediately. Followed by the Hado #4 Byakurai piercing through Ichigo's shoulder.
In Magical Girl Apocalypse, when Kii Kogami loses his shoes but must keep going on the rocky ground, he eventually passes out from blood loss and infections on his lacerated feet.
In This Ugly Yet Beautiful World, a barefoot Akari steps on broken glass and gets a cut. After the initial pain, she shrugs it off and wants to keep going, but Ryou stops to wrap her foot with cloth.
In Saint Seiya, during the battle against Virgo Shaka, Ikki is subjected to a heavy session of Mind Rape. He then sees an illusion of himself as a child carrying a baby Shun while walking barefoot on a valley of very sharp stones; Shaka's voice keeps asking him to drop the baby (which keeps getting heavier and heavier) and save himself, which he keeps refusing. A lot of attention is drawn to his feet soaked in blood.
In Fate/kaleid liner PRISMA☆ILLYA, Illya is in Synchronization with Kuro/Chloe. At one point, to stop Kuro from hitting on Shirou, Illya starts slapping herself in the face. When that doesn't deter Kuro, Illya stubs her toe, which makes them both collapse, clutching their foot and crying.
In The Seven Deadly Sins, Galan is defeated when his own power turns him to stone. Angered at the atrocities he had committed, Jericho kicks the statue, but only succeeds in hurting her foot.
Both the titular protagonist of Syun Matsuena's one-shot Haruka, Haruka Yata, and the elfin female protagonist who does not give her name, are barefooted during the entire story, the former because he was barefoot at home when he met the girl and ran outside so hastily when a villain attacked them that he forgot to put his shoes on, the latter because she just Does Not Wear Shoes and has already suffered some wear and tear from walking to his house in bare feet (which makes Haruka consider calling the cops on her). This lack of footwear becomes really problematic for the two of them when they end up outside, stuck on railroad tracks and stumbling over rocks and coal. To spare her more discomfort after the conflict has passed, Haruka carries the girl in his arms back to his house, even though she can walk just fine.
In A Certain Magical Index, one of the girls suffers from this when her feet fall asleep in the wariza pose and she begins to fidget them desperately.
In Naruto Shippuden, Sakura deliberately stomps on Kiba's foot when he almost spills the beans on a plan to capture Sasuke in front of Naruto that they were supposed to keep mum about. Worse, this is a universe where just about everybody wears open-toed sandals, and this is one of those very rare times we get to see the downside of that in action.
Seen in the fight with Zabuza and a few others when makibishi spikes (aka caltrops) are tossed onto the battlefields. Zabuza, however, was battle-savvy enough to avoid the ones in his fight with Kakashi.
At least one battle saw someone's foot pierced by a kunai.
In Future Diary, when Yuno gets ambushed by a another diary user trying to kill her, she makes the irrational mistake of taking her shoes off once she's indoors (it's Japanese custom/courtesy to remove outdoor footwear when entering a residence), not realizing he's set up traps for her to stumble upon barefoot, first in the form of thumbtacks, then in the form of a flooded stairwell with an electrical current sent coursing through her wet feet via a broken lamp light, nearly electrocuting her. It just goes to show that sometimes, good manners can get you killed.
A bit into first season of Sound! Euphonium, Reina makes the mistake of climbing Mt. Daikichi in dress heels because it was a spur-of-the-moment decision to go there while out with Kumiko on a festival night, who in turn is wearing a beaten up pair of unsuitable clogs herself. After a while, the ankle straps on Reina's shoes rub her skin raw and Kumiko gets worried. Even though Reina admits her feet hurt, she says she doesn't hate pain; Kumiko finds that kinda hot, and Reina calls her a freak. When the two reach the top of the mountain and sit down at an observatory, they both kick off their dirtied-up shoes and trade them for bare feet.