Dear Alex,
Thank you for reporting the issue.
It seems that when you draw a polygon on an orthomosaic some vertices are placed under the earth surface, which leads to the behavior you are observing.
What you can do at the moment is move misplaced vertices to desired positions, in order to do that select the polygon then click and drag the vertex to the desired position.
Meanwhile we will investigate the issue further and hopefully come up with the fix shortly.