The Bechdel test is a good rule of thumb but not perfect.
If you think about it - if in one entire movie two women don't even have a conversation it sounds pretty bad.
But I like watching sci-fi and for good or bad that mostly seems to have male dominated casts. I'm sure rom-coms easily pass the Bechdel test but I don't watch them.
I think in STID you had about 10 named men (if Keenser is male) and two named women so its pretty hard to get the woman-woman conversation in just as we didn't have a Scotty -Sulu, Adm Marcus- Chekov, Uhura-Pike, McCoy-Chekov, etc dialog