The real cause of the collision was poor seamanship and failure to follow the COLREGS on the part of the bridge crew of the destroyer. Most specifically they were seriously in violation of Rule 6: the Safe Speed Rule

http://navruleshandbook.com/Rule6.html

  Every vessel shall at all times proceed at a safe speed so 
  that she can take proper and effective action to avoid 
  collision and be stopped within a distance appropriate to 
  the prevailing circumstances and conditions.

The USS McCain was traveling at over 20 knots at the time of the collision, through a very crowded area at the entrance of a traffic separation scheme. If they hadn't been traveling at this obviously excessive speed they would have had the time to think, and to work through little UI issues like the one described here.