Search for miracle in a Matrix Universe

Let’s play with the popular Matrix scenario supposing that we live in a coded, artificial universe. In this case one of the most important questions is: Why we cannot able to observe any sound evidence of this fact?
Unless our mighty coder is either pathetically incompetent or he/she doesn’t want to unmask him- or herself, it is logical to expect some signs that points out that it is a constructed world.
These signs should be clear and apparent. In other words, they should be easily distinguishable from every other component of our world: A “miracle” seems to be appropriate for this purpose. Obviously, it should be really convincing: According to Hume, “no testimony is sufficient to establish a miracle, unless the testimony be of such a kind, that its falsehood would be more miraculous, than the fact, which it endeavors to establish”.
It was impossible to detect a “miracle” in the pre-scientific eras of human history, since it was possible to interpret any phenomenon as a miracle (and to attribute e. g. to a god) and science didn’t exist serving as a reference point. When everything is miracle, then a miracle has no distinctive function at all.
So it is logical from the coder’s point of view to hide such a kind of a “miracle” that can be detectable as a deep irregularity only after the beginning the era of the science. Optimally, it would be a very strange phenomenon remaining unexplained from the early experiments to date.
But according to the history of science, it is difficult (or even impossible) to find such a phenomenon. Neither planetary motions nor lightings are unanswered questions today, and although we have to face with some unsolved problems (e. g. the origin of life), we have better and better attempts to decode them. In accordance with this, every scientific era has different central problems from the theory of electromagnetism to the non-existence of ether. So: where is that mysterious miracle?
Perhaps logically impossible to construct a world both with intelligent beings and such a kind of unanswerable problems: We humans simply work out reasonable solutions for any irregularities (even they aren’t necessarily true).
Another possibility is that from our coder creator’s point of view, there is not a substantial difference between the science of the early 17th and the 21th century. He/she wasn’t able (or willing) to specify exactly the level of scientific knowledge needed to discover his/her signs. It would be a good piece of news for us, since it suggests that the future development of science will be enormous, and in comparison to the reachable level in future, there is no an essential difference between Galileo’s scientific knowledge and the string theory.
So it is possible that we still didn’t find that message-anomaly.
Or: we already found it, but we still didn’t recognize it as a quintessential “miracle”. My favorite candidate is the dark energy and I am really curious whether it will be an unsolved problem a million years from now.