How do I fix a video zooming glitch taken by iPhone?

I don't think it's a glitch, it looks like you're actually switching cameras, and as much as the two can be made to look similar, there will be inherent differences because of different optics. I don't have this issue on my phone, I wonder if it's older one that can't do the smooth blending as well? Also, it does look like maybe one of your cameras is a bit smudged since you lost contrast when the video switched, but the slight warping feels like it's because of different optics.

You could cut on the "glitch" and use a warping effect to try to blend the two together a bit more, but it would likely be easier to make sure you're not switching cameras when zooming. Anything that's not the default .5x, 1x, 2x, or 3x on your camera (depending on your phone model), is digital zoom and it's scaling up your video before switching to a different camera.