I think there are a number of problems with your question because it uses modern terms to describe the Middles Ages when such terms didn't exist at that time.

"Science" in its modern meaning only began to evolve during the Middles Ages, when philosophers like Roger Bacon and William of Ockham advocated methodological principles that would lay the foundation for the scientific revolution. But this revolution would happen during the early modern period, i.e. several hundred years later. Since science in its modern meaning didn't exist during the Middle Ages, "scientific truths" didn't either.

Moreover, from an epistemological point of view it's not quite clear that truths exist at all. At the very least, modern scientists wouldn't say their theories are absolutely true. There's always a chance that new evidence might come up and invalidate current theories.

That being said, there were certainly generally accepted facts. One might even call them secular (although that, too, is a modern term) since these facts weren't derived from the bible or they even contradicted the holy scripture. For example, parts of the Old Testament like Revelation 7:1 suggests that the Earth is flat. Yet the Catholic Church and Benedictine abbesses like Hildegard of Bingen had no problem with accepting that the bible mustn't be understood literally in this case. Educated thinkers at that time knew that the Earth was spherical.