User is able to apply retainer against one billing record in Create Batch Invoice screen, but not to other billing records.
This is because the retainer is for a specific project (project retainer), not for all projects of a client (client retainer). To resolve this, you must delete the retainer payment and receive it against the client instead. In some cases, you might have received the retainer payment against a phase. In that case, your issue can also be resolved by accepting it as the parent project retainer instead.