Yes atz75 is right about Aguirre seeing them do more and, as she says, it's in the book clearly.
He watched them with 10x42 binoculars..."for 10 minutes one day, waiting until they buttoned up their jeans... " So, yes, in the book, Aguirre saw that having some sort of sex and that pretty much carries over into the film with the "stemming the rose" comment, which is in the screenplay but not the book.
That was a clever way to get the idea that Aguirre actually saw them in the act though, wasn't it?