As the works of Aristotle and other authors translated from the Arabic became unbanned and began to be understood, this caused considerable tension in the previously insular Latin West. Albert the Great, Thomas Aquinas, and others worked to reconcile the two intersecting traditions. Secular masters of arts who were not theologians often concentrated mainly on reading the new texts as they stood — a tradition that continued through the Renaissance. The bishop of Paris issued lists of condemned propositions in 1270 and 1277 (see Wikipedia and Stanford Encyclopedia of Philosophy). Scholars generally agree that there was no coherent group or single individual targeted by the whole of the longer 1277 one, which also contained a few propositions endorsed by the not-yet-canonized Aquinas.
In the 20th century, Pierre Duhem influentially claimed that the 1277 condemnation had a large positive effect on nascent medieval natural science, by freeing it from the alleged dogmatism of Aristotle, but with more research, scholarly consensus has backed sharply away from this (although I think there is still some distance to go). This is a good example of the lingering effects of anti-Aristotelian prejudice. Contrary to the stereotype, medieval Aristotelians often cheerfully adopted new ideas when they seemed to have merit, and Italian Aristotelianism in particular was especially friendly to such developments.
A little treatise attributed to Giles of Rome (excerpt relating to Aristotle here) on “the errors of the philosophers” appeared around 1270. In other writings, Giles was by no means hostile to all philosophy, but here he focused on matters of theological concern at the time, with a bit more motivation and analysis than the actual condemnations. “Philosophers” refers with some specificity to the canon of falsafa translated from the Arabic.
As Giles analyzed it, the main issue underlying concerns about Aristotle himself lay in the principle that later scholastics referred to as “nothing comes from nothing”, and that Leibniz later endorsed as the principle of sufficient reason. Leibniz and others found this constructive-flavored notion implicit in Aristotelian and neoplatonic thought to be compatible with theological concerns. More generally, many theologians have found ways to read the broad spirit of Greek rationalism and naturalism as not inherently opposed to their concerns. Greek rationalism and naturalism, unlike many of their modern variants, were not reductive in nature. The thought of Aristotle in particular provides sophisticated resources for integrating concepts of immanent purpose in a rational account of the world that makes no special pleadings.
The notion of creation from nothing is itself a theological interpretation not literally present in Genesis, but creation in time is literally present, and many theologians have been reluctant to give it a figurative interpretation, even though broad principles of interpretation as far back as Augustine allow for figurative interpretation when there are issues with a literal reading. Aquinas, for one, took a diplomatic middle position that reason cannot decide between possibilities of eternal creation or creation in time, so he adopted a forgiving attitude toward Aristotle on the related question of the eternity of the world. I believe Aristotle and the neoplatonists on the other hand clearly thought reason did rule out a creation in time, and that this did not in any way destroy higher spiritual values. Personally, I want to say that they were right on this, so I respectfully disagree with the diplomatic Thomistic position, while considering it historically progressive in its context. (See also Fortunes of Aristotle; God and the Soul; Strong Omnipotence; Occasionalism; Pseudo-Dionysius on the Soul.)