When Annie hardened her leg and kicked Eren in the face, Eren started to bite down on the crystal until Annie started beating him in the head. However, when she was done, she just ran away. That was the perfect time to take him out of his nape and if she'd done so, I believe the female titan would've succeeded.
So, what was going through Annie's mind? Why didn't she take Eren out of his Titan when she kicked and beat him in the head during their fight in Stohess?