Indeed. I sometimes wonder if that's not what happened with my mom's aviary cockatiels. She raised them since before I was born, and even after being fed and handled properly as young, some still ended up with behavior problems. Near the end, she had so many breeder birds, it was hard to keep track of.
Yes, it is a common problem. Especially for people who first start to breed and often end up with babies without even knowing why or how... They don't mean to inbreed but unless you separate all the pairs or prevent the entire flock from procreating (and most people don't know how to do it, either), it's impossible to avoid.