First, every penny that you receive for late fees and utilities should be being entered into your tax return as income. The utilities should be offset with a utility expense and late fees are just cash in your pocket. They can call it utilities and late fees but if you get to keep it it is rent.
Security deposits are trickier but you can enter them as income and then expense them later if you return them. Or you can enter them on the return and then create a matching expense for "Security Deposit Held For Tenant" or something like that. Then you take the deposit into income later if the tenant loses it to you. If you keep it it is income, though..
Either way you should enter the actual cash that you received and spent for each of the three properties regardless of what the 1099-K says. You should figure out why there is a difference - if there is one after you enter everything as income that you should - and document it so that you can answer questions later if anyone asks. The schedule E will total all of your entries for all three properties and that should match or exceed the 1099-K.
@DGX
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