Our quickbooks keeps marking off invoices as paid when they haven't been paid, we reconcile with the bank account but it's automatically marking some off as paid

Hi maidtoimpress-ou Thanks for reaching out to us here on the Community. We'd be grateful if you can check if the payments that are being applied to the invoices are credits or unapplied payments. If they are then this would indicate that you have the 'Automatically apply credits' activated within the settings. To deactivate this function; Select the gear/cog icon > account and settings > advanced > automation > automatically apply credits > deactivate/toggle off > save.