Which of the following is the MOST likely reason that a list of control deficiencies...

The most likely reason to exclude control deficiencies from an IT risk register is that they have already been resolved. The risk register should focus on current risks that require attention or action.

While deficiencies with no business relevance (A) might be lower priority, they could still be relevant to the risk register. Actual misconfigurations (B) are definitely relevant and should be included.