Claire knew that the 'pharmacy robbery' couldn't be a coincidence the moment she saw the guns. This was happening the day that Alex lured the squad his old organization sent over? But she had to admit she hadn't expected this tactic.
At first she tried to think her way through it rationally but she was quickly blinded by panic. She wasn't able to control her emotions in the face of danger the way he was.
Her panic blocked out the fact that Ray was trying to negotiate with them until the gun shot rang out and grazed Rachel's arm. They were serious. They would kill other people to get to her.
There had to be something Claire could do to signal Alex! If he knew what was going on inside right now, he would have already come flying in through the window or something.