I was surprised to see Alyson Hannigan, the host of Penn & Teller: Fool Us, receive a Producer credit on the same show. The probable reasoning behind this got discussed in a thread here dedicated to the show, starting around Post #947.
I had seen the Mel Brooks movie High Anxiety many times before I realized the Bellboy (Here’s your paper! Here’s your paper!) is played by academy award winning director Barry Levinson. He was also one of the writers.
This threw me forever.
I get similarly thrown by the fact that the director for Jeopardy is Kevin McCarthy, who’s been dead for more than six years.
Of course, it’s a different Kevin McCarthy (and not the politician, either)
A million years ago I was at a friend’s house and the largely forgettable movie Cold Feet played in the background. When the credits came on, I grabbed the remote and rewound, shocked to see Tom Waits co-starred!
I rented the movie and watched it again.
Speaking of Mel Brooks, he produced the 1980 drama The Elephant Man but chose to go uncredited to avoid misleading (prospective) viewers into thinking the film was a comedy. Had he not done so, he would have been a perfect example for this thread. 
In the same vein, Peter Frampton won an Oscar for the makeup in Braveheart. No, not that Peter Frampton, but this one.
Some years ago, CBS decided to stick its feet into the world of live televised MMA bouts. One of the names in the credits caught my eye: Executive Producer David Dinkins.
It was actually David Dinkins Jr., son of the former NYC mayor.
Seeing Chuck Barris as the writer of Freddie Cannon’s hit song set in New Jersey “Palisades Park.”
Yes, THAT Chuck Barris.
A Major Motion Picture was shot partially where I work a while back (in my department). I was upset to see this doofus coworker got an on-screen credit, but that was tempered by the fact the movie sucked big time. I’m GLAD I didn’t get a credit!
Ha! I just watched “Victor, Victoria”, last night on TCM, for the first time, and noticed the name Peter Frampton on the end credits, and thought, wait a minute, he does makeup for movies too??!
I don’t think he actually appears in the credits, unfortunately, but for a few moments in Monty Python and the Holy Grail, the Black Knight is played by Richard Burton. No, not that Richard Burton. A local blacksmith of the same name, an actual one-legged man, who took over for John Cleese once the Black Knight has had both arms and one of his legs cut off.
Rumor has it that Cleese still likes to boast about the time that Richard Burton was his stunt double.
Not in a movie, but looking at the original cast of the Broadway musical West Side Story, I was shocked to see the name of Elizabeth Taylor buried well down in the credits.
This was years after National Velvet and Father of the Bride, so I knew it couldn’t be that Elizabeth Taylor, and it wasn’t. Francis Elizabeth Taylor was a dancer and sometime singer in the late fifties. She later married Miles Davis, and so became Francis E.T. Davis
I was surprised by a name not in the credits: in Cloudy With a Chance of Meatballs the voiceover artist for the character of Officer Earl was Mr. T. When the sequel came out with the same characters, I assumed it was the same cast as well but nope: according to the end credits Officer Earl was voiced by the ever-entertaining Terry Crews, doing a very good Mr. T impression.
(In a similar vein I watched Wreck-It Ralph and blindly accepted the Ed Wynn-esque voicing of King Candy…which turned out to be by Alan Tudyk (of Firefly fame). Wynn’s vocal stylings have become such a cliché that it didn’t even occur to me to wonder about it despite the fact that the man has been dead since 1966.)
Why? For the beginning of the end credits you’re actually watching Tom Cruise dancing.
That’s just how good the man is.
Rumor confirmed. John mentioned it during his performance with Eric Idle in Pasadena last November. 
I saw this on Youtube before I saw in on IMDB or listed as credits but Gates McFadden did behind-the-scenes work as a choreographer for Labyrinth (as well as Dark Crystal)
I used to get a twinge of sadness seeing the name “Nick Berg” pop up in the credits of music documentaries and similar shows from the 90’s. Later I discovered it was a completely different guy with the same name.
Many years ago on an episode of Rockline with Iron Maiden singer Bruce Dickinson, a caller mentioned that he’d seen Bruce’s name on a heavy metal compilation CD and wondered how he wound up with that gig. Bruce told the caller that it was a completely different guy named Bruce Dickinson, who was a mid-level manager and “reissue producer” at Columbia Records. This was more than a decade before SNL’s famous “More Cowbell” sketch.
Two more that don’t quite fit the definition of the OP.
I first heard of Levon Helm as an actor in one of my favorite movies. I didn’t find out until a few years ago that he was well known as a musician before his acting career. So I wasn’t surprised to see his name, but should have been.
I was channel surfing and came across a program on Discovery or NatGeo and there was some academic type talking about ancient Rome. I thought “hey, that guy looks kinda like Peter Weller (Buckaroo Bonsai, Robocop, etc.).” I watched a bit more and the next time he came on they had his name across the bottom of the screen. It was Peter Weller!
Peter Weller, surprisingly enough, has a Ph.D. in Art History from UCLA, focusing on the Italian Renaissance. He’s also taught history courses at Syracuse. Imagine taking a history class and having Robocop as your professor!