If you want to learn how counter breakers work in S3, read this post: A complete exposé on counter breakers: why they work, why they don't, and what you can do
If you are doing CBs too late, they won’t work. If you are trying to counter break the startup of manuals (including juggles), such that you are trying to catch timing lockouts before an active break window, they won’t work. But this rule applies to only manuals.
They work just fine in every other situation.