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It's possible, that since you went through a third party, rather than a county clerk's office, your registration renewal, didn't get entered, or it was entered incorrectly. But, more than likely, since that was the only reason you were given for being stopped, it means they ran your plates, possibly because of their age, and since it came back unverified, they made the stop. Car thieves, often steal plates from other cars, and put them on stolen ones,
Since there were two officers, my guess is that one, was in training. I don't know what the law is regarding getting new plates, but about every 5 years, my county clerk tells me I need new ones, and they provide them, for the same price as the sticker. Since you go through Tom Thumb, they may not have that option. JMHO