In Shame (1x04), Lois tells the Neighbours that they mowed their lawn in the middle of the night for 15 years to avoid talking to them, but in Flashback (2x25) they only moved in when Malcolm was born, who was 12 in Season 1.
In Sleepover (1x06), the timer in the boys room was set to 4:30, but after only 45 seconds of seemingly uncut video, the alarm went off.
In Francis Escapes (1x07), when Dewey throws stones at the 'sasquatch', they would never reach Francis:
-They never go above Dewey's head height, which is lower than the fence
-They would never even reach the fence with the angle he threw them at
-Francis wasn't that close to the fence anyway
Yet the stones hit Francis with a downward angle as if they had gone really high!
In The Bots and the Bees (1x14), Lois says to Spangler that Francis "nearly lost his life", yet later says to Francis that he "did not almost die"
In the Malcolm's Girlfriend (3x04) cold open, when Reese leaves the house his pants are briefly visible
In Company Picnic (3x11-12) Dewey's sugar problem is a major plot point, yet on multiple occasions throughout the series he eats ice cream (e.g. Hal Grieves (7x14) when Hal brings the ice cream trolley into their bedroom) and sweets (e.g. Smunday (1x15) while on the roof)
In Hal's Birthday (3x15), Stevie takes all of 2 seconds on the phone to tell Malcolm about going to the destruction derby, yet he wouldn't be able to say more than one or two words in that time
In Watching the Baby (5x02), Craig's badge is different, he has a gold one instead of a red one
In Malcolm Dates a Family (5x14), Stevie says he watched Abe torch his wedding album, but in Kitty's Back (6x05), Abe says he has a wedding album to tape back together
In the Family Reunion (4x03) cold open and in Blackout (7x07) the garage is full of junk, but in Tiki Lounge (6x13) and College Recruiters (7x12) it is clear and the junk has completely vanished