The universe coming into existence from nothing 14.8 billion years ago “contradicts” basically all of the presuppositions upon which science is based – i.e., that observable reality is all that is required to explain everything.
The origin of matter, energy and space-time is utterly inexplicable from the point of view of science – and yet that explanatory morass is the “conclusion” from the best of current science. So, being “left with a phenomenon that contradicts science” isn’t much of a quagmire, since science itself puts itself there.
All matter, energy and space-time came inexplicably into existence from a singularity, yet science can only appeal to what matter, energy and space-time will permit it to demonstrate with regard to matter, energy and space-time – the entire realm that is the legitimate concern of science.
Science presumes a whole lot in order to function. Those presumptions dictate what science can say. It would appear that science is far out on a very tenuous limb with regard to what it can and cannot say about anything – by its own admission and method.
Perhaps a “phenomenon that contradicts science” is one put in place by design to make you wonder about the efficacy and sufficiency of science?
*
“Our discreditable secret is that we don’t know anything at all, and our horrid inner secret is that we don’t care that we don’t.”
― Dylan Thomas*