Why didn't Annie take Eren out of his Titan when she kicked and beat him in the head during their fight in Stohess? 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?
There will be a second time skip in the manga, my knowledge is drawn from scenes shown after that.


   As it is shown in Reiners memories, Annie is part of team of Marley's Titan kids and they are on a mission, basically doing espionage. But very early one of them gets killed and Reiner convinces the remaining two that they have to come back with something substantial in exchange. In the course of their infiltration they indeed target Eren for abduction, however Annie is exposed without having much of a plan at the time, eventually realizing that Eren may have become a match for her. She is completely within enemies' territory and Levi's squad has shown her the enemy is quite capable of killing her. Having her cover blown was the worst thing that could have happen to her. Annie's primary goal at the time was to retreat and regroup, she was fully aware that any unnecessary action would be an opportunity for the enemy to incapacitate her. She only fought Eren at this point because she was aware he would (and effectively did) prevent her to escape. Maybe she also panicked a little.


However, I can probably summarize with: Fleeing was the most intelligent thing to do at the time.