This issue may be caused by a conflict with the Magento core code or a third-party extension. Here are a few steps you can take to troubleshoot the issue:
Disable all third-party extensions: Disable all third-party extensions and check if the pagination works with the filter option. If it does, then re-enable each extension one by one to find the culprit.
Check the template files: Check if the template files related to pagination and filtering have been modified. If they have, then revert the changes and test again.
Check the server logs: Check the server logs for any errors related to pagination or filtering. If you find any errors, then try to fix them.
Check the Magento core files: Check if any core Magento files related to pagination or filtering have been modified. If they have, then revert the changes and test again.
Check the database: Check if there are any issues with the database that may be causing the pagination issue. You can use the Magento database repair tool to fix any database issues.
If none of the above steps work, you may need to seek assistance from a Magento developer to troubleshoot the issue further.