From the Super Mario Wiki
Super Mario RPG: Legend of the Seven Stars
In Super Mario RPG: Legend of the Seven Stars, after Mario and Mallow join Geno while he is fighting Bowyer, Bowyer will retort that a three-on-one fight is unfair. To compensate for this, the , and buttons will appear in front of him. Bowyer will then fire an Aero at one of the buttons, which will effectively lock the ability to use that button's commands (magic, items or attacks). Only one button can ever be locked at once, although Bowyer will continually fire Aeroes at the buttons every few turns until he is defeated. His Machine Made counterpart does this as well.
Paper Mario series
This ailment in Paper Mario is inflicted by Spy Guys when they attack Mario with their hammers. The impact will dislodge one of Mario's action commands (jump, hammer or item) from the menu. Two boss fights also feature this status effect - Fuzzipede's tackle and Bowser's jump attack both disable one of Mario's commands. Lost commands are restored after a couple of turns.
Paper Mario: The Thousand-Year Door
In the second installment of the series, this ailment returns with the same effect as the previous game, but now partner abilities can be disabled as well. It is once again inflicted by Bowser's jump. Additionally, using the badge Jumpman increases Mario's jumping attack by 1 at the cost of disabling his hammer command, and Hammerman has the opposite effect.
Super Paper Mario
In Super Paper Mario, this effect is inflicted by Tech Cursyas. When affected by it, the playable characters cannot use their special abilities for a period of time. Mario loses the ability to flip, Luigi loses his super jump, Bowser is unable to breathe fire, and Princess Peach loses her parasol abilities. If Mario gets this ailment while already in 3D, he will be stuck in 3D until the ailment wears off, the timer runs out, or the player switches characters.
Paper Mario: Sticker Star
In Paper Mario: Sticker Star, the only time this effect occurs is in Rustle Burrow, where Mario is unable to use his hammer after losing it here. He is also unable to use any of the hammer stickers he has in his album. Due to the loss of Kersti, the Battle Spinner and Paperize are unavailable as well, which also occurs when she is eaten by Petey Piranha in Rumble Volcano.
Mario & Luigi series
Mario & Luigi: Superstar Saga / Mario & Luigi: Superstar Saga + Bowser's Minions
In Mario & Luigi: Superstar Saga and Mario & Luigi: Superstar Saga + Bowser's Minions, the Boos in Bowser's Castle can steal command blocks with their attacks, stopping the brothers from using them. During the last two boss fights with Popple, he can steal one of the Bros.' hammers, preventing them from using any attacks involving their hammers. In the Prima Games guide for Mario & Luigi: Superstar Saga, Prohibited Command is listed as four different effects: Jump X, Hammer X, Hand X, and Item X.
In Mario & Luigi: Superstar Saga + Bowser's Minions, Ludwig's boss battle restricts the brothers to using counterattacks to defeat him.
Mario & Luigi: Partners in Time
During the final battle against Shrowser, no command blocks are available and the fight can only be won by counterattacking.
Mario & Luigi: Bowser's Inside Story / Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey
In Mario & Luigi: Bowser's Inside Story and Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey, during the battle against the Vacuum Helmet inside Bowser, it will suck up one of the bros' command blocks, preventing either items or Bros. Attacks from being used. After a few turns or after the helmet is destroyed, the Bros. will get it back.
Mario & Luigi: Dream Team
In Mario & Luigi: Dream Team, Mario battles Thunder Sass while only being allowed the Item Command Block. Also, during the battle against Bowser Jr. in the Battle Ring, using a Bros. Attack will make Bowser Jr. steal it, disabling it until the bros get it back.
Mario & Luigi: Paper Jam
In Mario & Luigi: Paper Jam, when first exploring the Twinsy Tropics Dungeon, a group of Hammer Bros steal the bros' Command Blocks, and they must be battled in order to recover the stolen Command Blocks. The Kameks will also disable whichever Command Block has been most-used by each bro during their battle (e.g. if Mario mostly used Jump, Luigi mostly used Bros. Attacks and Paper Mario mostly used items, those Command Blocks are disabled for them for a few turns).