Is appealing to the Holy Spirit and Miracle a fallacy?

This reminds me of magic. All throughout history, humankind has been inserting "magic" as the "best explanation" for things we don't yet understand. If we had reliable evidence that magic existed (any kind of magic including God's magic) then making this assumption might not be such an egregious error in reasoning, but it is, and here is why: Countless times when we attributed the unknown to magic a non-magical explanation was later found to be far greater in explanatory value-- never has the reverse been demonstrated . This fact alone undermines the whole idea of magic. We should not ignore the possibility of magic, but our standards for accepting such an explanation should be in proportion to the probability of such an explanation being true. The problem is, those who believe in magic have used fallacious reasoning in the past to continually affirm their belief in magic, making the probability of magic, from their perspective , irrationally high.

So to answer your question I would say, yes. In my opinion, until someone can empirically distinguish a miracle from magic, it would be an appeal to magical thinking. See Magical Thinking