Square treats MassageBook credit card processing fees a bit differently than fees processed directly in Square. For card-not-present transactions, the fee is split between two categories: API and Application Fee. When you're running your reports, ensure that both of these items are included. A good way to spot check this is to find a transaction on your MassageBook report, locate it on your Square report, and ensure that the fee in Square totals to the fee you see in MassageBook. If it doesn't match up, the report is not displaying all of your fees.
When you run a Square report from your Square dashboard > Reports, select Filter By and ensure that you have all Sources selected, as shown below.
Point of Sale refers to transactions processed via your Square POS app only. To view any credit card payments where you or the client manually entered in the credit card number (referred to as card-not-present transaction) you must select eCommerce Integrations from the Source dropdown.