If you bought something online with a debit or credit card and did NOT log into your Paypal account then of course it won't show on that Paypal account because you bought as a 'guest buyer'. However your seller may have processed that payment using their Paypal 'card reader' and so Paypal would show on your bank or card statement.
If that is not the case then contact customer services AND your card issuer to query the transactions. However if its listed as well in your paypal account then could it be a part payment for an item when you didn't have enough funds in your balance so they took the rest from your card?
Advice is voluntary. Kudos / Solution appreciated.