Eraser noticed pretty quickly that someone was warping in so why didn't he cancel out Kurogiri's quirk as soon as he saw him and take him out when there was only one or maybe two of them? He and Thirteen shouldn't have had much of a problem fighting two villains when only one has a power, and he noticed almost immediately that something was wrong.
He firstly had to alert everyone because, apparently, no one else noticed until the first batch of villains started to came out. I'm pretty sure that the element of surprise worked against them, and since he was with a bunch of newbie students, his thought process was much more conservative.
A lot of times, while under pressure with little time to react, the best options might not come to our minds until way after such event has occurred. Nevertheless, his call was still very good since his students were his number 1 priority.
An example that compliments this; imagine a Samurai fighting while protecting his students compared to that same samurai fighting without any clear distractions. The exact same setting, moreover, you can expect his thought process to very different.