To date the only real anomalies are the sudden dramatic promotion of a senior NCO to a LtCmdr and the fact that Shepard is always addressed as "Commander", whether she's a Lieutenant Commander or a Staff Commander. Still, even that is consistent as, for example, Kaiden is only referred to as "Lieutenant", not 2nd Lieutenant, 1st Lieutenant or Staff Lieutenant. So just going by the dialogue, he could be either one (though officially he was a Staff Lieutenant.)
That's pretty standard in militaries though. Calling a Lieutenant Commander anything other than Commander in conversation is a big faux pas. Same goes for different rates of Lieutenant.