I think the line “we received an imperial encoded transmission” and “the message was sent by your father” are lies. If we trust cassian shooting that bloke on the ring of Kafene then those two lines work as deception of the truth that cassian was fed info then murdered the informant. It is a cover story for evil deeds
I also think Jyn is in shackles because they think she is possibly a traitor.
I feel this really explains the tone of those scenes.