It's not her fault and just highlights the problem with her being lied to by everyone. Joe has a partner that is trying to do her job with no knowledge of important facts. As far as she knew she was dealing with and admitted murderer who faked his death with no body ever found that had broken into a lab recently to steal some stuff. She told this fugitive to stop and put his hands up, instead he moved forward while holding a gun shaped object, things went wrong. If Joe doesn't trust her enough to tell her the weird stuff that's going on, even if he leaves out Barry's identity, he shouldn't have made her his partner.