It happened again after Bligh was appointed Govenor of New South Wales. Within a few months after taking command, his military subordanant placed him under arrest as part of the Rum Revolt. Clearly, there was something lacking in Bligh’s command skills.
My own take is that the problem with Bligh wasn't that he was too cruel, but that he was too lax compared to other captains when it came to discipline and punishment. He couldn't maintain order among a crew of conscripts, most of whom didn't want to be there and many of whom came from criminal backgrounds. Poor leadership and interpersonal skills were to blame rather than inordinate cruelty (contra the Hollywood version of things).