You did not post your system, so it is a bit hard to figure out what is going on, especially when you say that you see poles moving to RHP in Spice.
Going purely on the plots you provided (poe zero map primarily) I tried to construct a model that would create similar plots.
sys=zpk([2.4*10^9*j -2.4*10^9*j], [-0.0000001 -11.5*10^7+1.2*10^9*j -11.5*10^7-1.2*10^9*j],-100000000);
subplot(121);bode(sys);grid;
subplot(122);pzmap(sys);
xlim([-1.5e+8 2e+7]);
The first subplot shows full bode plot. If you focus on the region you are looking at, you will see similar plot to what you show:
subplot(121); bode(sys, {1e+9*0.1034 1e+9*2.8278}); grid;
Now if you zoom in bode plot magnitude that looks similar to your plot.
If you do
you will see phase margins at first two crossovers are negative and phase margin at 3rd crossover is positive.
If you do
you will see the system is stable because all poles are in the left half plane, even though one of them is essentially at the origin.
Bottom line: even though you see negative phase margins, this system is stable, as all poles lie in the LHP. Hope this helps.
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