Lt. Commanders are usually referred to as 'commander' when addressed, or 'Lt. Commander' durimg something, like a trial. They are not just called 'Lt.' while at the Lt. Commander rank. This has been true for all the shows in the franchise.
I guess it's always safer to 'round up' a rank than to 'round down' if you don't want to run the risk somebody takes offense. (Also because I think in this case 'Commander' is the main rank, and lieutenant in this context approximately means 'deputy' or 'substitute' AFAIK).