Why does this dialogue appear in the transcript but not the episode?

Question

The Chakoteya transcript of DS9: The Maquis, Part I contains a long chunk of dialogue between Sisko and the Admiral.

S2, E20 ("The Maquis", part 1, third last scene [Ops]).
SISKO: I'm hoping I don't have to remind the admiral how many people pass through here during a week's time. It's not possible to keep tabs on every single person while they're on the station.
ADMIRAL: If I didn't know you better, commander, I'd think you were just making excuses [...]
ADMIRAL: Don't bother me with details. Just clean up the mess, Commander. And quickly. Before this becomes a permanent stain on your record. Do I make myself clear?
SISKO: Yes, sir.

But in the episode I notice only 3 seconds in which I weakly hear Sisko say something like:

I am fully aware of the situation, we are facing...

and immediately after, leaving this up in the air, I hear Bashir saying,

What do you think they're telling him?

Why was this cut in the video? Is it a mistake?

Valorum · Accepted Answer

This is explained in the Deep Space Nine Companion. In short, the scene was written to explain to Avery Brooks (Sisko) what he's supposed to be portraying, emotionally speaking. It was never intended to be heard by the audience, except in brief.

The top of Act 5 features Kira, Odo, O’Brien,
Dax, and Bashir standing around in Ops, comment-
ing on a conversation taking place between Sisko and
a Starfleet representative via com in his office. They
can’t hear what he’s saying, but the heated tone of the
conversation is obvious. In fact, a scene was filmed
and later cut, in which Sisko follows up on the close
of the conversation by picking up his desk monitor
and throwing it to the floor.
Wonder what got him so steamed? The addendum to Scene 47 is a scene that was never intended to be heard by the audience but was written to give
Avery Brooks something to play against.
This is the dialogue Sisko is having with an
admiral on the monitor in his office. We neither hear
the dialogue nor see the Admiral on the monitor.

You can see the full scene in the original script (listed as an addendum).

This is an ADDENDUM to Scene 47.
It should be placed after the Pronunciation Guide in the script.
This is the dialogue Sisko is having with an Admiral on the monitor
in his office.  We neither hear the dialogue nor see the Admiral on
the monitor.
We do see Sisko trying to keep his temper while emphatically
responding to the Admiral's heated inquiries.
They are mid-conversation as the scene begins...

Why does this dialogue appear in the transcript but not the episode?

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