That is true, Nick, she did. Vader must have been put priority on finding her after their confrontation earlier this season. Perhaps since she was disgusted by the Jedi way, she could be swayed to become an Inquisitor and right hand (perhaps overthrow the Emperor)? But it still doesn't explain why the Sister was hanging out. All that was needed was a line of dialogue when she was with her probe droids (why have they come to my lair? or My leads have paid off). Who knows, maybe Wolffe is still a loyal to the Empire clone?
The Viper probe droid managed to gather a good deal of intel from both the Phantom and the old AT-TE before it was eventually taken out. I think it's entirely possible that some of the information that Rex, Wolffe and Gregor had in their computers was transmitted to the Empire.
Filoni actually dropped a hint in Rebels Recon about the Grand Inquisitor (the Pau'an who was voiced by Jason Isaacs). He said that we had actually seen him in episode(s) of CLONE WARS. I know that some Pau'an's did appear in CLONE WARS, including some of those episodes that only existed in storyboard form. But is it possible that he was one of the Force sensitive infants that was taken by Darth Sidious?