Final answer:
The error with subject-verb agreement in the sentence is 'flow,' which should be corrected to 'flows' to match the singular subject 'river.'
Step-by-step explanation:
The sentence in question contains an error with subject-verb agreement. In the sentence, 'Beneath Puerto-Princesa Subterranean River National Park in the Philippines flow an underground river that empties into the Pacific Ocean,' the verb should agree with the singular subject 'river.' Therefore, the corrected sentence should read, 'Beneath Puerto-Princesa Subterranean River National Park in the Philippines flows an underground river that empties into the Pacific Ocean.'