I think he mis-interpreted what Hugo was saying... in that it was just a job, and didn't have the time or desire to get into the fandom/franchise beyond that.

Perhaps fans on global sites were pointing fingers at Bay as if he was the reason why Hugo was not "able" to get more involved in the role or character, and Bay was responding defensively to that criticism... but really, a voice-over role that only took an hour doesn't require any character-research on the part of the Voice Actor.

Since Bay took down that comment, maybe he later realised that he was just drawn into something that wasn't his fault... this time at least.