- What was that cave whose gate the pelicans pushed Mahito through? Why were they in such a hurry to get there?
- Why did Natsuko go to the other world to give birth, and why was she so angry at Mahito for showing up?
- What was the heron's deal? Why did he draw Mahito into the other world in the first place? Why did he pretend he could bring his mother back by creating a fake duplicate?
- Why was Mahito told not to touch the dolls when staying with Kiriko?
As for the twist, I'm assuming you're referring to the reveal that Himi is Mahito's mother traveling in time. To me that didn't even register as a twist, because there was so little setup or foreshadowing for it. IMO one of Spirited Away's weakest points is how the ending reveal about Haku is handled, and Himi's reveal had even less setup. It came almost completely out of left field, and was dwelt on so little that I just went "oh, okay I guess".
And while we're making comparisons to Spirited Away, because it's IMO clearly the closest to this, The Boy and the Heron's worldbuilding is significantly weaker. Spirited Away gave you plenty of time to take in what the world looks like, where things are, their scale, and also hints at a much larger world beyond the bathhouse. TBatH by comparison is basically just a sightseeing tour. We never get an idea how big these places are or what, if anything, else there is in them besides just the things we see. It's all left incredibly vague, because the movie seems to come up with rules as it goes along. When it feels like anything can happen, all meaning and weight disappears from the story, and you're just left waiting for the next ludicrous thing the movie can throw at you.