Your clients should not send you 1099-MISC if they paid with a credit card.
You can refer them to this text in the instructions for the form 1099-MISC:
Payments made with a credit card or payment card and certain other
types of payments, including third party network transactions, must be
reported on Form 1099-K by the payment settlement entity under section
6050W and are not subject to reporting on Form 1099-MISC. See the
separate Instructions for Form 1099-K.
By sending out the 1099-MISC, your clients are essentially saying that they paid you directly (check or cash) in addition to the payment they made with a credit card (which will be reported on 1099-K). In case of an audit, you'll have trouble convincing the IRS that it didn't happen. I suggest asking the clients not to do this to you, since it may cost you significant amounts to fight the IRS later on.
In any case, you report on your tax return what you really got, not what the 1099 says. If you have two 1099's covering the same income - there's no legal obligation to report the income twice. You do not have to pay twice the tax just because you have stupid clients. But you may have troubles explaining it to the IRS, especially if you're dealing with cash in your business.
If you want to avoid matching issues, consider reporting all the 1099s, and then subtracting the duplicates and attaching a statement (the software will do it automatically when you add the description in the miscellaneous item) about what it is.