I'd always figured (based on offhand comments by Ev and his investors at the time) that it was because Ev had difficulty taking a hard-line on people for performance issues. The quote I'm thinking of was something like "Evan always wanted his friends to share in his success", and it was in the context of hiring friends or promoting internal employees into larger roles rather than looking outside the company. My read on that is that he placed a very high premium on loyalty, rewarding people who had helped out Twitter when it was very young, while the board wanted to capitalize on its hotness to bring in big external talent that was available then.
This would also be consistent with the employees feeling a significant amount of loyalty toward Ev, and several wanting to quit when he was ousted.