Well, either she was unable to remove all of them, she didn't locate some of them, or the Borg collective communicates in ways that go beyond simply the implants.
She couldn't remove them all actually because that would have been too inconvenient for the movie script. After all....they couldn't just have Picard be the most respected captain of the fleet with the best ship at his disposal to boot. No, they had to have him suddenly develop some superhuman capabilities as well that allowed him to telepathically "feel" what the Borg was up to. Hmmmm. Funny how none of those abilities showed up in post Best of Both Worlds conflicts with the Borg on the TNG show. Then again the Borg Queen never made an appearance either during the whole TNG run.
Don't think about this too hard, folks. It never made much sense.