You might be recording costs on the job/project that are not billable to the client using the General Journal screen. From here, you can associate the journal entries with certain account types to the projects and the same then reflects on the project's profit or loss. These entries affect the financial reports like Profit and Loss, Balance Sheet, etc.
However, in general, it is not a good practice to enter project expenses via the G/L entries. Instead, you should enter such expenses via the Vendor Bills, Expense Entries or Checks screen. Otherwise they will not reflect on the project reports or Projects > Performance tab.