You can only create separate invoices for the expense item and the timesheet if you are using the Detailed Expense option.
The system will automatically create a separate invoices for each timesheet and expense sheet, if on the client record you set both the Billing Cycle and Invoice Grouping to Timesheet.
If you are using any other selection on the billing cycle and invoice grouping you can still create separate invoices by overriding the invoice grouping when you select to create the sales invoice.
From the Create a Sales Invoice drill down into the list of items to be included on an invoice by selecting the Items value
This will give you a list of the Timesheets/expense items which are available to invoice, now select just the expense items or timesheet items required and select to create the invoice.