Are there specific terms for crop that has been ruined in some way? I'd especially enjoy a word/phrase for produce/crop that has over-ripened or rotted away.
There are no specific terms for rotten crops, but you can use many of the synonyms of rotten. One common term is spoiled to indicate the crop is no longer nutritive.
With the men off to war, many of the farms' crops went unharvested, and lay spoiled and rotting under the blistering summer sun.
If the crops have been destroyed by disease, you can instead use blighted
The pestilence spread rapidly through the fields, leaving large swaths of blighted crops in its wake.
As with most words, it can be used figuratively:
But Ahab's glance was averted; like a blighted fruit tree he shook, and cast his last, cindered apple to the soil.
As in the above example, a pestilence is a plague-like disease that can be used with agriculture. You can also use withered to describe crops that are damaged and dying and generally unusable.
Infestation is another, although more often used with things like insects rather than bacteria or fungi.
Not related to crops, but certain foods, particularly those that are fatty or oily, can go rancid.
She rummaged around his refrigerator to try and find something to eat, but all she found was a wide assortment of condiments and a stick of rancid butter, that must have been left there by the previous tenant.
Other foods, such as milk, can sour, and still others (bread, fruit, cheese, etc.) can be covered by fungi and become moldy. This also can apply to some crops that are susceptible to fungal diseases.