Willow Run,
Oh, yes they have. In the IO, during the Iranian "Hostage Crisis" an F-14 landed on the wrong ship.
A two-ship, led by a visiting HQ pilot, launched into the haze, flew its mission and returned to "a" ship. The visiting pilot mis-identified CV-64, the Constellation, for the one they left. Being a "visiting" pilot, filling the square of being "the troops" he wasn't very current. To the break they flew, on downwind, neither crew noted the error. Visiting pilot got a wave-off, at which point his RIO noted the wrong number on the island, informed said pilot "wrong ship, xxxxhead". Off they went to the right ship. Poor wingee didn't catch the number at the 90, being well practiced, he trapped. Instantly, the deck crew figured it out, as did the wayward Tomcat crew. Taken to the brig for the night, a ransom demand of ice cream was made. Next day, a helo dropped off a load of ice cream, the -14 and crew launched off, thoroughly zapped and that's the end.
My brother was pre-flighting his Tomcat when it happened, but I'm sure there are others.