User has a phased project with the project rules Send as joint invoice and Always show in Create Batch Invoice screen set for its phases. However, the user also set the billing rule Minimum Bill Amount to $1.00 in the Invoice Filters and Options dialog. Now the phases with nothing to bill (zero value) still show up in the Create Batch Invoice screen.
This is the expected behavior in CORE. The project rules always override the billing options. So the phases will always show up for billing. If you want to prevent this from happening, you need to remove the rule Always show in Create Batch Invoice screen from the phases so that they don't show up unless there is something to bill.