John Gill Commentary Ezra 9:13

"And after all that is come upon us for our evil deeds, and for our great guilt, seeing that thou our God hast punished us less than our iniquities deserve, and hast given us such a remnant," — Ezra 9:13 (ASV)

And after all that has come upon us for our evil deeds, and for
our great trespass
As famine, sword, pestilence, and captivity, for their idolatries and other heinous sins:

seeing that our God has punished us less than our iniquities deserve ;
for they deserved eternal punishment, whereas it was temporal punishment that was inflicted, and this moderate, and now stopped; the sense is, according to Aben Ezra,

``thou hast refrained from writing some of our sins in the book of remembrance, and thou hast let them down below in the earth, according to the sense of thou wilt cast all their sins into the depths of the sea;'' but Jarchi better, ``thou hast refrained thyself from exacting of us all our sins, and hast exacted of us beneath our sins (or less than they deserve), and hast not taken vengeance on us according to all our sins:'' and has given us such deliverance as this ;
from captivity, which they now enjoyed.