It sounds like you should be OK, as long as you're not relying solely on the 1099s. I always used them as a reference that I could crosscheck against my records, but the number I reported was the actual income I received.
There are penalties for the company that fails to send out a 1099 on time, depending on how late they are:
http://smallbusiness.chron.com/happens-1099s-late-17332.html
As far as how to report them to the IRS:
http://pocketsense.com/report-late-1099-irs-6470982.html
The company that sent an incorrect (overstated) 1099 may have just fallen into that year-end situation of when they cut the check and when you received it, since it's not income for you until you actually have it in your hands. Unless your records show that the amount they reported is vastly greater than what you received from them plus what they still owe you for work done last year, you might consider contacting the IRS.
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