Problem with sales invoices and customers i think its a bug

this is not a bug. this is how Manager works now.

if you are selecting the invoice number when receiving payment, then allocate the exact invoice amount to it. else it will be shown as overpaid.

else you can leave the invoice number blank when receiving the payment and let Manager allocate the payments across the due invoices.

you can read about this in the following topic

click the figure 2 against the inventory item and check the transactions related to it.