The word crop has several meanings. As a noun it is a swelling on the body, or any rounded or swollen item, for example a bird's gullet, the seed head of a ripe plant or the the rear end of a horse. As a verb it means 'to cut the top or sides off' or 'to gather in' (as in cereal crops). A less well-known meaning is 'to protrude from the earth's surface'.
The context of early printed examples of the term 'crop up' doesn't help us decipher whether that 'crop' is an allusion to the growth of crops or to the 'swollen' meaning. That is because the things that were first said to have 'cropped up' were rounded items which protruded from the ground, i.e. rocks.