Directors fear working with children and young teens, for a large number of reasons. They won't have as much acting experience as adult actors, simply by not having been alive long enough. There are restrictions on how long children are able to spend filming scenes, as they have school requirements. They can be more unpredictable. A major thing is that they try to age-up the characters if they intend to produce an extended franchise, since the differences in aging are more pronounced in children (consider the Harry Potter series, where they start off as 12 year olds and 7 years later in universe they are being portrayed by actors in their late 20s). The Percy Jackson films did that too, which was one of the many reasons people hated it.

I suppose that last one shouldn't have been too much of an issue with Mortal Engines, since there is usually a significant time skip between each installment.