At least that's my best guess. I have not seen this prior to this semester but I've seen it a dozen times in the last week, always with iPhones.
The frames appear to be playing out of sequence. E.g. frame 1 then frame 3 then frame 2. But Tracker does not pause on frame 3. So doing a single frame advance in Tracker causes the tracked object to jump ahead and then fall back to an intermediate position.
I'm not quite sure how to interpret this because I'm not quite sure what is actually happening. But it only happens with iPhone video so it has to be something screwy with Apple. Usually, so far, retaking the video fixes it. But I'd rather not deal with it at all.
I'm having this issue too. Can someone please offer suggested fixes? I'm about to assign my students to use Tracker and most will be recording the video with their phones. Will converting the video format possibly help?
(Edit) I found converting it to mp4 from mov solved the problem.
I had to make a profile to reply to this problem, we've had a lot of troubles with this in my course, but I finally figured out the best way to deal with it: If it's a slowmotion video, make sure you edit it before you export: make the entire video slowmotion (by dragging the slowmotion sliders out to fill the entire vid), otherwise it will remain the weird transition. Then you have to open your Photos app on your Mac, and in the app you mark the videos you need and you go to edit and export it at the highest quality (not original though), and then the file is still a .mov, but the metadata part that makes it jitter is gone. And make sure you change the frame rate in tracker to match the one from your video (slowmotion is 240/s) in Tracker. This works for me, and I haven't had any troubles since doing it this way :) No matter how much conversion I did with transmute, handbrake, online tools, it kept happening regardless of the file type. This is the only way I found worked, and it's probably the simplest too :)