Matter does not always behave in a way science currently understands. Are these instances miracles, or made up stories?
Okay, I guess you are.... How's this for an answer: neither. Actually, since miracles are just made up stories, so you've given no real choice here as they are the same thing. Miracles are claims that things happened in a way that we know is impossible. What you are describing by saying, "Matter does not always behave in a way science currently understands," is matter acting in a way which we don't understand or can't properly model, but which is knowable and possible...
Get the difference: one we don't understand and the other we know is impossible.