It all depends weather what you plead guilty to is crime or not. It seems like a it's a small regulatory offense, and probably a violation. I 'd say you should be ok.
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To qualify for naturalization you need to show good moral character for the last 5 years. Even if you were not convicted for shoplifting, if anywhere in the record you admitted to the elements of the crime immigration could use that to make a determination on your moral character. Probably that's the reason they are still looking at it, to see if anywhere on the record appears an admission.