What they did was excercise what is known as the "Right to Offset". That basically means that if you owe money from one account and have it in another they can use that money to "offset" the amount you owe. Now, unlike other fees this is one where you really can't plan for it happening as to exactly when. So it can cause other problems.
However, your attitude really makes it hard to have much sympathy for you. After all you are getting upset at them for their poor customer service when you knew you that you owed them money. You have had around 2 Years to pay them back if you really did want to. You say that they didn't send you any information to pay them. Well I bet that they did. When you first went delinquent I am sure you got letters and/or phone calls about the amount you owe. But let's say that they NEVER sent you anything. Why didn't you contact them if you really wanted to pay it back?
Oh and I have news for you. EVERY bank has that same clause in the account terms. So if this happend at another bank, it would have probably been the same result. Just like Chase, they wouldn't inform you in advance either.