Well, isn't Misaka a bit dumb/naive at this point of the story? It will take a while for her to grow and this arc is probably here to show off this growth. This is technically her first infiltration into a government lab, even though it was abandoned so she's learning. In a way, this is just one arc that is transforming her from a naive little girl into well, a capable heroine of this series.
The other girls on the other hand.....
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