Hi Collette,
Yes, whenever you receive a payment from someone via Paypal, Paypal takes a percentage from the payment you receive. This is done any time you receive money...it does not matter whether you invoice someone via the Paypal system or by sending them your own invoice.
Here is a link to the PayPal Transaction Fees page:
https://www.paypal.com/us/cgi-bin/we...ide&countries=
The section titled: Fees for receiving purchase payments will apply to the question you are asking.
I hope this helped!