Yes, this happened to me after I cleared CdO. I think that during the battle against 63 enemies, a grenade or two got a police man or guardia. When I initially got the mission, I didn't stop anywhere, so I don't know if I would have had the problem before the battle.
There's a thread on this forum about buying Amnesty from Calderon. I bought one to get on the government's good side, then rebels ($100K). Now I can go anywhere until I choose sides.
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