Yeah, one of the many problems Rogue One creates as opposed to answering.
I would rather say it exposed a problem as opposed to creating it, since Rogue One didn't introduce
that much as far as the Empire's knowledge about the Rebels is concerned than Star Wars already did. The battle of Scarif was in the crawl, and everyone on all the ships – whether engaged in the battle or taking the plans – were clearly, and to Vader, rebels. That they had been at the rebel base is only revealed to the audience in Rogue One, but it's a reasonable assumption for Vader even without Rogue One. I guess slightly more uncertain, as it still left the possibility they were communicating at an arms' length with Leia's ship (a possibility that had never crossed my mind until it was asserted in Rebels), but there should have been at least an attempt to question everybody,
and prisoners from the unnamed mentioned battle in the crawl as well.
I take it as whenever you expand on things, it leaves the rest of the story with less room to manoeuvre and expands its problems, so I don't mind it at all since I like more story, but I also why I don't like such expanding for sole the purpose of
explanation. Explanations often make the thing that was being explain less likely, since they tend to go into specifics. There were million ways it could have happened, congratulations, you explained it, because of it now there's only one way, and we don't buy it!
Now we need a movie to explain why they
needed the mind probe for Leia, and why Vader couldn't use the Force while we're at it. Not.