Ptolemy's "Almagest", a classic astronomy book that's been used throughout the Middle Ages included Earth being a comparatively insignificant point in the universe. People had already known about Earth not being the outer space's focal point in the times of Dante, St. Augustine, Thomas Acquinas and more. What do you know, these big Christian thinkers had no problem fitting this scientific fact, the one that's later become supposedly so "problematic" to religion and such a shutdown answer to Christianity. It almost like Christianity cares not about astronomy, huh.
Evolution was not claimed to be false. The Pope said it is a scientific theory with some validity to it. And that's exactly what it is, nothing more, nothing less. It's a theory about how the changes in the organisms could have changed across time. But then it became the religion of "EVERYTHING works in this particular way". Our brains, our societies, our laws, it's all based on the "adaptability" mechanic. Sure, a lot of it makes sense, especially the biological stuff. But it's not a be-all, end-all answer. At most Christianity may say "it's a theory, not a confirmed fact" and "it doesn't and shouldn't claim to answer any questions fro outside its stated field - live organisms' changes across time" and "it doesn't have all the answers" and especially "like anything scientific, it will provide no 'why', only 'how's". If that's "believing evolution isn't real", well, I guess you've scored a point.
The Trinity doesn't make sense? Would a cube make sense to a 2D being? Try to explain that one. I mean, it's made of squares, you know what those are, but they are connected with each other and create a bigger shape... No, no, the squares' lines don't cross, they meet at the ends... No, seriously, that's what 3D means, it's not "impossible".
If God made sense to our little human brains, it would be a very disappointing God. I would doubt such a God could've been the Creator of all things in the first place. After all, a character in the story is no more capable of writing the sequel than they are of tearing the pages their story's printed on. But Jesus was somewhat of an author cameo, except in a more real way than any allegory could sufficiently express. Still, doesn't mean the Author wasn't "separate" in some way, while still being the same God.