To reproduce:
1. Open project repro
2. Open scene "repro"
3. Set the scene view to 3d
4. Select "plr". It's a sprite with a polygon collider, it's z position is 2
5. Hold shift to edit the plr's collider and hover over a long line (to add a new point) - notice how the new collider point get's rendered as if the z position is still 0 (not on the collider line, but in an empty space in scene)