I figure it's reasonable to say Nepgear attacked before Blue Sky was going too fast to catch.
Honestly the counterattack is the weakest part of the omake since it's the most unlikely, Blue Sky would totally fire and dodge, but everything else just leads to Blue Sky blitzing her way to the command center, killing everyone there, and then picking off VIPs until Sega shows up. Best explanation I have for the not dodging is probably that she's still rather dazed from Nepgear's initial attack, it took ~49% of her health, and the explosion it casused.