In my experience at least, doubt is not often something that is welcomed in church contexts. It's sometimes accepted, but often a cause for concern. Occasionally someone makes the point that we need to have doubt in order to have faith.
There are at least four passages in the canonical gospels where they record someone/some people doubting in the face of the miraculous. I suppose there are far more if you count the enemies and opponents of Jesus, but in most of these cases the doubt is a result of their predetermined decision not to believe in Jesus.
The most famous one is, of course, the disciple Thomas in John 20. I don't want to dwell on him too much. Firstly because being the obvious one I am sure that everything that can be said about him has been somewhere by someone. But secondly, some scholars suggest that this is actually the author(s) of John trying to smear the growing sect springing up around the (emerging) Gospel of Thomas. From a Bible films point of view however, it's noticeable that he nearly always gets a raw deal. If this scene is to be included then you can bet your bottom dollar that Thomas will express some doubts earlier in the film as well.
It's possible that this incident is also referred to in passing by Matthew. The second passage I want to cover comes from Matthew 28:16-17
Now the eleven disciples went to Galilee, to the mountain to which Jesus had directed them and when they saw him they worshiped him; but some doubtedMatthew's "some" suggests that Thomas was not alone. Perhaps John focussed in on him to increase the drama of his narrative (though I suppose Thomas's doubts were before he had seen the risen Christ). What I find interesting though is the way the comment is casually thrown in and remains without comment. These people are seeing the risen Jesus, and yet still they doubt. But there's no shock horror, no rebuke. They were there, they saw everything everybody else did, they just still had their doubts.
What's also interesting is that the suggestion is that these people worshipped in spite of their doubts. Furthermore the next verse is even more telling because Jesus includes them in his commissioning. They have their doubts but Jesus still values them and their contribution. It's significant that these other doubters never appear in a Jesus film.
The third passage I want to look seems to be evading me for the minute. I think it is also in Matthew, and as it's the one that I noticed most recently.
Lastly there is John 12:27-30. Jesus asks God to glorify his name, and God replies "I have glorified it and I will glorify it again". We're told the crowd heard it but whilst some attributed it to an angel some said it was just thunder. Again this is intriguing because it seems like the kind of occasion when it should have been easy to draw a consensus. And yet some heard the voice of God or an angel; others just heard thunder. This passage appears in 2003's "Gospel of John" but nowhere else as I recall.
What's I find intriguing is firstly the way that Jesus seems to be fine with the doubts, at least on these occasions. But more striking is that the case is often made by atheists today that people in Jesus' day were likely to misattribute unusual natural occurrences to the hand of God. But the Bible provides evidence several times that people were both willing and able to suggest alternative explanations for supernatural events. Scepticism isn't new, but significantly, in the latter two/three cases it also doesn't seem to be a barrier for following Jesus and being included by him.