Most movie trailers do not have footage from the finished product. Usually parts or most of the movie is filmed and then given to editors to make a teaser trailer. The rain was digitally added in AFTER they gave that footage of the train to the editors. I've seen "mistakes" like this in movie traliers before, it's just how Hollywood works.
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Remember that Hogwarts is in the highlands of Scotland, over 500 miles from London; it's quite possible (indeed, it's very likely) that the two places have very different weather systems. I once went to Blackpool for the day, and rode from brilliant sunshine and fine weather in London to torrential rain in Blackpool ("only" 250 miles away), then back into good weather on the return journey.
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