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Looks like you're wiping out the mapboxgl-marker class when you change className, which I presume is used as a selector to handle positioning of the markers.
mapbox-gl-js version: 0.43.0
Steps to Trigger Behavior
A demo of this behavior is available here: https://codepen.io/anon/pen/jYMBRq
Expected Behavior
Markers shouldn't move from their coordinates while zooming.
Actual Behavior
Markers move from their coordinates while zooming.
Notes
I think this same bug was previously reported in #5133 and #5151 (I modified the CodePen from #5151 for my demo), which were both resolved by #5139.
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