It can mean there's a problem, or discomfort, but it doesn't always mean that.
If your baby is crying, it doesn't mean you're doing anything wrong. It doesn't mean you're a bad parent. It doesn't mean bub's unhappy. It's not something that you always have to feel must be stopped, because sometimes you can't stop it. Sometimes, all you can do it put up with it, or try to offer the best comfort to your child you can.
However, if your baby cries every time you pick it up by its ears, you're doing it wrong.