Thanks for your question.
It’s a bit difficult to give a simple answer to your question as there are a number of very different situations that you could be asking about.
If you are asking, ‘is it wrong to have, at various times, doubts about whether there is a god and whether the miracles in the Bible occurred?’ then there is nothing wrong - lots of people have doubts. Doubts are just a symptom that there is something that needs to be addressed in our lives; perhaps there is an area of our understanding where we simply need more information, perhaps there is an aspect of our lives that is at odds with following Jesus that we don’t want to change. The key in these situations is to seek answers - read the Bible, ask God to give you understanding, speak to a Christian Bible teacher, with Christians that know you well (or that can get to know you). Often it is through the process of having doubts, and seeking answers to our doubts, that we actually grow in our understanding and faith.
There is also a healthy ‘questioning’ that followers of Christ are encouraged to have with regard to miracles and the people that claim to perform them. Jesus warned (for example in Mark 13:22-23) that there would be people who claimed to have divine authority and insight, who would perhaps perform impressive “miracles”, but whose teaching, in the end, would not be what the Bible taught and who would lead people away from following Jesus.
The most important thing about asking questions and seeking answers the being willing to change your point of view on the basis of those questions and answers. Much of the harm of organised religion comes from the demand to believe in certain things without questioning. Such “blind” belief is not biblical. If God is true and the bible is true then it will always stand up to our questions. But if it is false then our questions will make that clear and we can walk away from it.
So there is a questioning of God that is wrong, that arises out of a commitment to a worldview that denies even the possibility of miracles and God - a commitment to ‘fault finding’, if you like. The problem with this position is that is those who hold it often fail to apply the same level of skepticism and critique to their own assumptions and beliefs that they apply to the evidence surrounding the existence of God and the miracles in the Bible. A number of people who I have spoken to who claim to be atheists fall into this category. This is not a questioning that seeks answers, it is a questioning that merely seeks to maintain and confirm its own presumptions.
I am not sure if this addresses the issues you were wanting dealt with Hannah, so feel free to ask a follow up question.