Hello there, @linzishanklandwo.
Welcome and thank you for joining here in the Community. Let me assist you with the invoices.
So far, we haven't received any similar issues reported. QuickBooks Online offers automation features, such as automatically applying payments to an invoice.
If this feature is turned on and your customer has an available credit, this will automatically link to your open invoice and mark them as paid.
To turn off this feature, here's how:
If you want to unlink the payment, see the steps below to complete the process. Here's how:
For additional information, you can click this article: Record invoice payments in QuickBooks Online. This also provides steps on how you can record a partial or joint payment in QuickBooks.
Please refer to this article on how you can use the credit toward an invoice, refund the customer, or enter the overpayment as a tip-in QuickBooks: Handle a customer credit or overpayment in QuickBooks Online.
Please know that you're always welcome to post if you have any other concerns. Wishing you and your business continued success.