There are a couple of reasons that the numbers might not appear as you expected.
There may still be studies that require a vote to be cast in Title and Abstract screening or in full text screening, or data extraction may not be complete for all studies. The PRISMA flowchart is updated during the review process. You should wait until all screening has been completed before exporting your PRISMA flowchart. Check the Team Settings for overall progress.
Covidence is study-based. If you have merged studies you will see that both the number of references and the associated number of studies are reported. Your Import History page reports the number of merges that have occurred.