Thank you.
The cache plugin does not itself cache any queries. Instead other plugins or WP itself must decide to cache a query.
The plugin installs an object-cache that makes the WP object cache persistent.
So can you say when scripts/queries fail?
I have written a script for retrospective data collection (user activities and etc). It takes a long time to execute the script (contains a lot of db queries), so it runs in the background in chunks. It works fine without APCu plugin, but when the plugin is active at some point it just stops executing with no error messages.
One more problem. I have installed the stage and prod environments on the same account of a shared hosting, and there is a conflict when both environments use the APCu plugin, which causes the server to freeze. However this is not a big problem, I just turn off the plugin on one of the environments.
You can set WP_APCU_KEY_SALT in each wp-config.phpto something that is unique for each install (like an md5 of the MySQL host, database, and table prefix). That could fix the issue with multiple installs.
Is that script in a plugin or theme?
You can use the APCu groups tag to see what data is in the APCu cache.
If it is not stored there you probably have another issue but it is difficult to tell from here.