Something similar happened to me. I got through the conversation with the two Stormtroopers, however, but had to leave to work right after the conversation, so I backtracked to the save point just outside.
Resuming my save just a few moments ago, however, I cannot open the opposite side gate for whatever reason. I remember the prompt being there before I left, though, and I think I even opened the second gate before saving but I don't remember for certain.
EDIT: I also have to mention that I did NOT receive a warning like OP did.
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