Phase margin is 90 degrees but transient step response shows overshoot
I suspect you're looking at an artifact of the propagation delay through the op amp.  The output overshoots because the effects of the negative feedback aren't felt until a finite time period after the response to the step.

If there's a propagation delay of N ns, the step response won't produce an effect on the output until T=N, and thus the feedback won't produce an effect until T=2N.