The latest version (22.10.10) is fixing this issue. Basically Debit Notes and Credit Notes should have been included which is now fixed.
Also, Journal Entry has new checkbox
(maybe too long. will need to figure out shorter label)
This will allow journal entries to be selectively included on cash flow statement. There is another topic in ideas category which will eventually allow to mark any balance sheet account as cash account. This would mean Manager could generate cash flow statements (besides other financial reports) with just journal entries. This would be useful if Manager is used as a report generator in its most basic form (without enabling any modules).