Both bad beats and lucky wins are coming. You mentioned above a situation with 89 vs AK, where you probably think AK is some huge favorite. Today I lost a hand as chip leader with AQs, one player went all-in with A9o and another player called with JJ. A9 hit a miracle straight tripling his stack, beating both of us who were ahead.
These situations (similar to winning with 89 vs AK) are more likely to happen in chip leader vs shortstack then in a situation with 2 players with similar stack sizes. Therefore, you get the feeling that system favorizes chip leaders but that is hardly true .