If she is the rank of Commaner, and the position of first officer, it's almost impossible that this is her first time in command.
Have you considered have her be a more junior officer? Maybe a young Lieutenant, the third or fourth officer in the chain of command?
Then she could be more inexperienced, and unsure of how to handle the emergency that's confronting her. During TOS they were always sending the senior officers down to a planet.
Especially if it's a relatively small ship, there might only be a small compliment of officers to start with.