User blog comment:Marcymariehunter/ME2 and Kaidan/@comment-217683-20101120003615/@comment-730941-20101120025214

We could assume that Shepard's personal charisma ('leadership abilities') somewhat negates the rank difference also - every squadmate magically seems to defer to the Commander's leadership, even if they are vastly more experienced or of a higher rank. I agree that Shepard's leaving the Alliance makes Alenko's rank irrelevant, but it would be interesting to see how this is treated in any future encounters.

As for Tali's reference to Shepard as 'Captain', this is a quarian custom rather than an actual promotion - any leader of a ship in quarian law is a Captain, who has the responsibility to represent their crew, and so on.