In missing cases the NPC has to be actually missing, yes. Elizabeth visiting the Agency isn't one, but I might fix it.
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Thank you for fixing the bug, but I think that you misunderstood the meaning of the word "alibi". See https://www.merriam-webster.com/dictionary/alibi for a dictionary definition of that word. Basically, if someone can be proven to be elsewhere when a crime that requires that person's presence for that person to have committed the crime, that proof is an alibi that shows that the person could not have committed that crime because the person was absent when the crime was committed.