In the fourth Harry Potter movie, as well as in the fourth book, the magic ceiling of the Great Hall reacts strongly with a storm when Moody enters. But since the Ceiling reacts that way to evil, wouldn't we expect it to react the same way to professor Quirrell carrying Voldemort on the back of his head in the first film?
In the books, there's absolutely no canon evidence that the ceiling of the Great Hall "reacts to evil". It's simply enchanted to mirror the actual sky outside (a point that is repeated throughout the series); there was a storm - totally unconnected to "Moody" (Barty Crouch Jr. using Polyjuice potion) - raging outside on the first day of term in Harry's fourth year.
If it did react to evil then it would have done so every single time "Moody" entered, which was not the case. He also would have been caught immediately, rather than being able to pass himself off as Moody (tricking even Dumbledore!) for an entire year.
In universe, it was essentially a coincidence that the storm was particularly fierce at that moment. Out of universe it was used for the effect to heighten the fierce appearance of the character.
For related reading, I've addressed a similar topic over on the Science Fiction and Fantasy Stack Exchange too.
As far as the movies are concerned, it could be that they wanted to hint that there was something "off" about the character, and decided that using the ceiling was a good way to do that. However, since the fourth movie was made later and presumably the workings of the ceiling were closer to what's described in the books (or ignored entirely) in the earlier films, this ended up introducing an inconsistency that isn't present in the books. As far as I'm aware there's no good in-universe explanation - using information from either the books or the movies - for why the ceiling wouldn't react to Quirrell during Harry's first year if it was enchanted to react to "evil" people entering the Great Hall.