To expand a little, purchase invoices are denominated in the currency of the supplier. If a supplier has invoiced you in two currencies, you need to create two separate suppliers, each with its own currency.
It would be unusual for a supplier to invoice in two currencies, so I assume you actually have invoices from two separate suppliers. So, as @Davide wrote, you need two distinct purchase invoices. On the one from the supplier who actually provided the goods, enter the item quantities and the cost from that supplier.
On the purchase invoice for the other supplier, select the same items, enter the costs, but insert zero quantities. This way, your inventory counts will be correct, but the extra costs will be added to average cost of inventory. For more information, see the Guide: https://guides.manager.io/9610.