Unfortunately this is a long standing design bug in Manager. It corrupts Tax reporting if receipts or payments are used with a negative line item without using Manager’s invoices. Applicable in all jurisdictions where any thing more that VAT sales offset by purchases (ie only the net difference) must be reported see:
or journal entries are used with tax codes see
The underlying issue is Manager guesses if a line item is a sale or purchase based on if it is a credit or a debit rather than using any transaction level information (eg linked to a customer vs supplier, or it is a receipt vs payment, or the user flags it as a sale vs purchase).
Resolution in Manger probably will have to wait for this idea to be implemented but it has been in the ideas category for some time and already has considerable votes
In the interim a cluddgy work around is possible but it involves giving up localizations such as Concept BTW rapport completely.