That isn't nearly enough to go bye. What kind of BoPs? Which Science Ship? Which weapons and powers were the BoPs using? What about he Science Ship? How experienced at PvP are the BoP players? The Fed Sci player? Were appropriate countermeasures used?
I'm not a great PvPer, but I can beat at least some Federation players in their Science ships. The really good PvPers will clean my clock no problem. I've seen good PvPers on both sides defeat multiple opponents.
Science, in the right hands, is an incredible thing but in general balance is pretty close to right. The Ablative Armor on the Intrepid-R is suspect but can be countered in a 3 on 1. As the others have said, there really isn't enough information to go on. Just try to remember that the pilot makes a big difference. Calling for a nerf out of frustration is never a good idea.
Shields resist can get insane on Science ships and drive attackers a bit crazy - I am guilty of the "ungodly schields resist" approach myself; However, it's the only thing science vessels really have; Strip it off, and they blow up if you look at them too long. On the other hand, the damage output is risible - I guess that the ship you talk about barely laid any damage on any of the BOPs.
To tell the entire story, I was in a good game last night whose result didn't tell the full story (15-1, but we had to sweat to get the kills), and even the Defiants' shields simply wouldn't buckle...