Were you still with an active Global Entry membership when you arrived at ORD this most recent time? Did you have a conditionally-approved GE application pending when you arrived at ORD? Was this travel done on a US passport?

When the facial recognition at the GE machines doesn’t work, then pulling up the traveler via passport for processing is what they continue doing. But sometimes at ORD they have been asking all GE members to show the passport while they also may ask some old school questions of the GE members who used the GE kiosks. I’ve not had a CBP employee at ORD ask me for fingerprints, as an active GE member without any conditionally-approved GE application waiting for finalization.

Import of citrus fruits into the US is very restricted. Your declaring the limes preemptively before being randomly selected or targeted independently for secondary/ag inspection should mean your GE membership status is unaffected by declaring the limes so that they can be safely stored and discarded. After baggage claim — but sometimes at baggage claim — CBP/Ag at ORD sometimes has asked for passports to note down whom and what they’ve processed — it’s never led to a problem for me — or just check it out of curiosity or to buy time for observation.