That bug has been fixed and the next version will be released soon.
Edit: Thanks!

We do not have it enabled in the first place, to allow users to ensure they have added the domains they would like to keep on there first. Otherwise, we would get complaints about cookies being automatically deleted, potentially without a way of restoring them, that should have been kept when they haven't configured it yet.

The next version is in the works which will fix this as well as some other bugs.

EDIT: Thanks!

Hello, You can disable the popup by disabling notifications. We have notifications enabled to let you know when we are cleaning up cookies by default, just in case there may be instances where cookies were cleaned when you think it shouldn't be. With the enabling of the cleanup log and counter as well, you can even restore the deleted cookies that it has removed at that point.