As the error message helpfully tells you, you need to use in_
against the foreign keys instead:
User.query.join(User.person).filter(Person.id.in_(p.id for p in people)).all()
Since you're going to query for both anyway, might be better to do a joined load and then get the people using Python:
people = Person.query.join(Person.user).options(db.contains_eager(Person.user)).limit(3).all()
users = [p.user for p in people]