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The following events actually happened but were mistaken as April Fool's Day pranks. No joke.

On a Tea Break (2006)
Holiday-makers flying back to Britain from Tenerife were told by their pilot that they could not land because an air traffic controller was on a tea break. The passengers initially thought his announcement was an April Fool's Day joke, but it wasn't. The plane had to circle for almost half an hour before the air traffic controller came back to work.

Stupid Safecracker (1960)
An attempted robbery was reported in El Rio, California. A burglar spent hours using an acetylene torch to try to cut open a safe in the Leonard Anderson Well Drilling Co. office. When he failed at this, he tried to guess the combination. Finally, he gave up and left. Fred Rush, manager of the company, commented, “He just wouldn’t believe the sign. We put it there because we don’t know the combination. Now the joke’s on us. When the yeggman tried to work the combination he set the lock and now we can’t open the safe ourselves.“ The sign on the safe which the burglar ignored read, “This safe is not locked.“ It wasn’t. [Los Angeles Times, Apr 2, 1960.]

There’s an elephant in my yard (1960)
George Morris of Safford, Arizona woke to find a full-grown elephant eating lilies in his backyard. He assumed it had to be some kind of elaborate April Fool’s Day joke. It wasn’t. But when he called the police to report the animal to them, they initially refused to believe he was telling the truth. Finally they sent over some officers. It turned out that “Dumbo” had been accidentally left behind by a circus that had pulled up stakes the night before. The circus was notified and a van was sent to pick up Dumbo. [The Ada Evening News, Apr 3, 1960.]

Four Perfect Bridge Hands (1959)
At London's St. James' Club, on April 1, four perfect bridge hands (a full suit) were dealt at the same table. The odds of this happening were estimated to be 53,644,737,765,488,792,839,237,440,000 to 1. The players had to convince other club members that the perfect hands were not a hoax. The duke of Marlborough, with 13 spades, held the winning hand. [Chicago Daily Tribune, Apr 3, 1959.]

Jurors believe summons to be a joke (1959)
Residents of St. Joseph, Missouri who received a notice on April 1st informing them they had been selected for jury duty thought the notices were a joke and none of them showed up. Deputy sheriffs had to make a special trip to their homes to inform them that the summons were real. The Sheriff's Department later made a special plea to the circuit judges: "Please don't draw a panel of jurors on April Fool's Day again." [The Chillicothe Constitution-Tribune, Apr 3, 1959.]

Firemen Don’t Respond (1950)
When fire station No. 2 in High Point, North Carolina received an emergency call from fire station No. 1, they decided not to respond, thinking it must be an April Fool gag. They were incorrect. It turned out that fire station No. 1 really was on fire. An explosion had resulted in flames which damaged their truck. [Waterloo Sunday Courier, Apr 2, 1950.]

Escape of the Duke of Lorraine (1632)
According to French legend, the Duke of Lorraine and his wife were imprisoned at Nantes. They escaped on April 1, 1632 by disguising themselves as peasants and walking through the front gate. Someone noticed them escaping and told the guards. But the guards believed the warning to be a "poisson d'Avril" (or April Fool's Day joke) and laughed at it, thus allowing the Duke and his wife to escape.

This story is occasionally offered as an early example of the custom of April Foolery. However, there is no evidence the story is true.

Extracted from here.