I think there are three possibilities:
1. Fredo tipped a contact in the Cuban government when he said at the party, "I'm gonna get me a real drink..." Recall that Fredo'd been to Cuba before--at the Superman show, when he made his fatal slip-up, he said, "Johnny Ola took me here."
2. Mrs. Roth tipped the military, after returning to her and Roth's hotel room and finding Johnny Ola dead.
3. We can assume that, since Roth had arranged for Michael to be driven from the party in a military car "for his protection," someone high up in the military (or his pal Batista himself) was in on the plot to kill Michael. When Roth failed to show at the party and wound up in the hospital instead, that high-ranking person put two and two together (those military guys looked to be in a big hurry to get to Roth's hospital room).