I usually get it when I reuse the license on a "staging" site on the same server that I only use for a few minutes before a deploy. Might be worth checking in IIS if you have any developer that has added another new site that contains the license too?
This morning we experienced some license issues on one of our customers pages. We utilize a multi site solution, and this message appeared in turns on one sites different languages. To clarify, one out of 5 sites showed the message in some or all (not sure) of its languages. I'm 100% sure the 5 site limit isn't violated :)
What are possible explanations? I explored the MultiSiteRestriction class and notice that it depends on MachineWideValidation. Is it possible that the machine wide validation had some faulty state?