Yeah, it's a general problem that can go unnoticed unless you're aware of the tell-tale sign of "seat of your pants writing".

Growing up reading comic books kind of trained me to notice when someone or something takes one moral stand or characterizes a character one way, and then does the opposite later when they think no one's looking. But when you're doing "SOYP writing", the only thing you're focusing on is "How can I make the audience feel what I want them to feel right at this moment?" So if your goal in writing is "Batman Is Always Right, No Matter What", you can have one story in which he beats up the Justice League for trying to play God, but then reveal that he has weapons of mass destruction stored under Wayne Manor "just in case" that get used to save the day, with no one calling him out for it because "Batman Is Always Right, No Matter What". (Or, insert any superhero here.)