My experience is all over the place.
At airports, many times I have mentioned “apples and bananas” and passed without further questions.
At land crossings: I remember the border in Montana, where oranges were allowed, but not their peels. The lady explicitly say she had to destroy them; my kids have been laughing at that for years. Coming from the South, we have had a (single) mango confiscated. One time they took all our fruit. Another one, the lady said “you guys will surely eat all this on your way to Canada, won’t you? ” and she let us keep it all.
Concerning fruits and vegetables: here’s the USDA’s page on how to get a permit. The form itself is here (PDF), and doesn’t even seem to require a fee. The usual processing time is 30 days.
However, a permit probably wouldn’t have helped you. The USDA’s Fresh Fruits and Vegetables Manual (PDF, 500+ pages) lists which fruits and vegetables can be imported from which countries. It appears that guanabana/soursop can only be imported from Grenada (and then only as a commercial shipment); and guava fruits can only be imported from Bermuda and Mexico (and only as commercial shipments from the latter.) Anything that is not explicitly listed in the manual appears to be barred completely.
If it’s any consolation, the permit would have let you import durian, mangosteen, and pineapple, among other things. Whether you want to have a durian in your luggage is another story.
You fruit WAS inspected. You showed it to the customs officials, they inspected it, determined what it was, determined that it was not allowed without a permit (as per https://epermits.aphis.usda.gov/) and thus confiscated/destroyed it.
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