I've been following the Rebels cartoons quite closely but I can't rule out that I may have missed something. Excluding the trailers (which are really just a collage of snippets from different episodes put together), I don't recall any particular scene where the rebels discover Thrawn to be the identity of their enemy commander.
All I can recall, in chronological order, is that:
- When Hera first rescued her father on Ryloth, his father merely spoke of the Imperial occupation being taken over by a new commander, in a way that suggests he is unaware the commander is Thrawn. Nobody in the Ghost crew appeared to have any inkling of the same, suggesting they probably do not know about him yet at this point.
- The first known contact was when Hera encountered Thrawn later while still on Ryloth. She recognised his rank but there's no indication she knows exactly who he is, since he wasn't called by name.
- Commander Sato appears to have a history with Thrawn. There's no indication if or when he had shared the information.
- By the time the Rebels started planning a large-scale attack to liberate Lothal, they had already firmly established the enemy commander as Thrawn. This is the first known moment to me when the rebels identified Thrawn by name.
So when did the rebels discover that their main enemy commander is none other than one of the greatest generals in Star Wars history?