No, that's right. Because you're an engineer, you get the best possible engineering station for your rank which is a commander station. The others are only Lt. ones because they're of the other classes.
I am a captain with 1 lieutenant tactical station, 1 commander engineering station, 1 lieutenant engineering station, and 1 lieutenant science station. This doesn't seem right. How do i fix?
Stations are based on the type of Ship you fly as well as your Rank. If you're flying a Cruiser you get more Engineering BO Skills. If you're flying an Escort you get more Tactical BO Skills, and if you're flying a Science Vessel you get more Science BO Skills. Your Captain is in a Cruiser, thus he gets 2 Engineers (1 at Commander and 1 at Lieutenant), 1 Science Lieutenant, and 1 Tactical Lieutenant.