Now I've noticed this sort of thing happens more often than not. Every now and again when someone acknoledges Captain Janeway's request, if they don't say "Aye Captain", or "Yes Ma'am", they sometimes slipup and say "Yes Sir". I've noticed Tom Paris ,Tuvok and Ensign Kim do this every now and then.
Another thing that muct be taken into account is the mood of the captain. When she is angry ar annoyed and gives an order that is very serious, usually paris will say "Yes, Sir" as oppose to ma'am.