A lot.
Children with emotional issues, learning difficulties, trauma, mental health issues. There's so many variations to the dynamics between child and parent, not everything functions perfectly for everyone. It's not rare. It's just that people who experience this as parents, usually don't speak about it to other parents. Not many people want to openly discuss something like this, because they usually fear being judged and side eyed by people who have no understanding of what having a difficult situation like that is really like.
There may well be an issue with the step-mom, but it's also very believable that the child could have thrown a tantrum, argued and ran away. I also would put no stock in what the bio-mom or bio-mom's family would have to say in regards to what the child would or wouldn't do, simply because of the awkward dynamics between biological father, step-mom and bio-mom.