Thanks for your message and welcome to the community!
In terms of the invoices that are marked as overdue but have actually been paid off, did you match up the payment transaction to the invoice?
In QuickBooks, when you receive payment from a customer for an open invoice, you need to make sure to match it with the invoice itself in the bank feed.
When you go to the Banking tab, select the payment transaction then select Find Match.
You will need to find the invoice in which the payment matches up to in order to close off the invoice and to avoid it showing 'Overdue'.
Alternatively, you can also manually create the payment transaction to close off the invoice by going into the invoice, then selecting Receive Payment.
I hope this clears things up for you, let us know if you needed further support.