I believe the biggest problem is the lack of honesty and greed of the owners of the exchanges.
let's take an example of yobit and let's go back in time:
January 05, 2015, 05:13:19 PMYoBit.Net - CRYPTOCURRENCY EXCHANGE & MultiCoin DICE - Free Coins every 1-24 hrssee that @YoBit was very active in the forum, do you know why he was very active in the forum? because he probably didn't have many clients and nobody knew about yobit. But when many people started using yobit, he began to see that he was making money, he became arrogant and a big greedy dishonest and scammer. As I said: The biggest problem is the owners of the exchanges who are dishonest and greedy. Honestly, these exchanges are not reliable... I like binance, but I wouldn't trust much money in these exchanges
Lets say 60-40% between honest owners to greedy ones even into those reputable exchangers we cant still be sure that they arent making any anomalies or shady transactions behind.
Dishonesty and greed is one of the most common problems next to security vulnerabilities.They know they can be rich in an instant if they do tend to steal all its users funds or ran away with it.