There's three versions: 24FPS 2D, 24FPS 3D, and 48FPS 3D.
You most likely saw the 24FPS 3D version, unless it was specifically advertised as "HFR". The main aim of HFR is to make the 3D work better and not give the usual headaches, etc. people get when watching 3D.
I haven't actually seen the 24FPS version yet, but I imagine there's a possibility the 24FPS version has a much faster shutter speed than would typically be seen in a 24FPS movie, which could give it a 'poor fps'/jittery feel like that you experience in a PC game with low FPS.
Ironically, I saw the 48FPS 3d and that made it far worse. Any scene with motion was literally unwatchable with both eyes open - and this was true for every one of my friends that went that night. We suspect it was something wrong with the projector itself, as the 3d previews at 24fps looked fine. I'd really like to see it again properly if the operators get things straightened out, as the low-motion scenes looked incredible.
Contrast that to Avatar, for example, which was an awful 3d experience for me as well, but mostly because I was stuck in the front row (I arrived "only" an hour early)
I saw the 2D-only version and there wasn't anything particularly jittery about it. It had the usual special effects issues with physics of unrealistic things looking, well, unrealistic (especially apparent in the dragon attack and the long shots when everyone is trying to run out of the troll mountain), but I didn't notice anything amiss that I could attribute to the 48fps->24fps down-conversion.
Either the 3D/24-fps combo makes things weird or JungleGymSam saw the movie in a place with a janky projector.
It was labeled as HFR and cost me a few extra bucks at that. Thinking back more I do remember a few scenes where I felt like things were smoother. Perhaps my expectations were too high or other people are simply way more sensitive to the effect?
There's also an IMAX 3D version. IMAX used to be filmed on 4x larger film stock, but now that everything is digital, I'm not sure if the IMAX version is different than the standard 24FPS version.
You most likely saw the 24FPS 3D version, unless it was specifically advertised as "HFR". The main aim of HFR is to make the 3D work better and not give the usual headaches, etc. people get when watching 3D.
I haven't actually seen the 24FPS version yet, but I imagine there's a possibility the 24FPS version has a much faster shutter speed than would typically be seen in a 24FPS movie, which could give it a 'poor fps'/jittery feel like that you experience in a PC game with low FPS.