Unless you elected to be taxed as a corporation, yes, that was a mistake.

But as long as you gave them the EIN you will be using on the SMLLC, it shouldn't make a difference on your return. You should give them an updated correct W9 though.  You can print one form the IRS website and fil it in and send back to them.

Thank you! Yes, the W9 all my clients used has my EIN on it, but I'm now realizing that several didn't issue me 1099s because of the S-corp classification. I assume I need to report the income I earned from these clients, but how can I do that correctly at this point?

Just report your actual income.  You never should rely on a 1099-MISC.

As a side note, you should be entering your personal EIN (in your name) on the W-9, *NOT* the EIN of the LLC.

How to enter 1099 and Cash income from Self Employment

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