It sounds like you may have the beginning of a new topic here.
May I suggest a re wording and then you may propose it.
There are many things which methodological naturalism (a basis for the scientific process) can not explain. I suggest that these may be considered to be real miracles. I would like to see how these can be denied.
Notice that I removed the reference to science documenting them as miracles. If you leave that in you will be expected to show such documentation and you will have a very difficult time doing so.
I think this would also work better if you gave some specific examples of what you are talking about. You may, alternatively, leave those for an early post of your own when you are asked for them.