Training can reveal various aches and pains that you didn't notice before. Years of bad posture or small strains here and there just from living life can add up.
Once you start a training program it isn't uncommon for these previously unnoticed issues to become very noticeable. Unfortunately there are many people that will blame the cause of the issues on the training.
One of the most common things I have seen in clients is knee pain once a significant amount of weight has been lost. The pressure that was on the knee joint for years has now been drastically changed. The issues that may have been hidden by pressure now have free reign to irritate the hell out of you.
This is one reason why it is important for your training to be adaptable. A training method that got you to a certain point may have revealed an issue of some kind. At that point it is necessary to change the methodology of training to further your progress while not creating more of an issue.
Exercises and training methods often get blamed for causing certain joints to become "bad".
Squats (or insert any movement) most likely didn't give you bad joints. The variables that go into why a joint hates us at any given time is far more complex than what movement pattern you did. It's easy to get discouraged when we have pain. In many cases the answer is to change a few things in your training so you can still make progress.
Don't be quick to villainize a movement or training methodology. It could be an injury that was there before, bad technique, poor movement preparation, too much intensity, too much frequency, not enough targeted recovery, and I could go on and on.
The biggest part of my job as a coach is modifying training so that my clients/athletes can continue to get results. Coaching is problem solving for other people. I love it.