I ran into this exact same problem today. Took me hours to figure out that it was a simple slip-up on my part.
I’m guessing you’ve discovered the answer yourself by now, given it’s been months since you posted your question, but I wanted to reply with my own solution anyway, just in case someone else comes along wondering why the duplicate frames.
For me, the problem was simply that I forgot to change my shutter speed. I left it at 1/50 when I switched from filming in 23.976fps to 59.94fps. By using a shutter speed that was slower than the frame rate, the camera had no choice but to default to capturing in a frame rate of 30 (the best it could manage at that shutter speed), but still played back at 60 (hence, the duplicate frames). As soon as I changed the shutter to 1/125, the problem was fixed.
A tiny little overlooked detail that had me scratching my head for hours….