Dialogue from a deleted scene found in the shooting script (scene 27) for the two dock controllers stated, "Excelsior and Intrepid are cleared to depart. Open spacedock doors", followed by the failure of both ships to power up and the doors to open, due to influence by the Whale Probe.
Two spacedock control LCARS graphics, ultimately not used in the film, confirmed the presence of the two Constitution-class vessels, as they clearly showed two berthed class vessels of which one was labeled with the registryNCC-1707, abbreviated to "NCC-177" on one of the graphics. As the graphics showed NCC-1707's departure vector alongside that of Excelsior's, has made NCC-1707 a very good candidate for Intrepid as it corresponded with the dialog in the deleted scene. The NCC-1707 registry originated from FASA's Federation Ship Recognition Manual (second edition, p. 11), at that point in time still considered an official reference work, where this Intrepid was listed as the refit-configuration replacement of USS Intrepid (NCC-1631), lost in the Star Trek: The Original Series-era, mentioned as such in Diane Duane's novel My Enemy, My Ally.
The ship (or ships) in question can be seen in two different FX shots. The first is a glimpse of a badly-damaged saucer section, and the second is a that of the secondary hull. The two parts appear in different portions of the scene, which would indicate either two different vessels, or one ship that was cut apart by the Borg or that performed a saucer separation maneuver.