I've been testing around and it seems they are extremely sensitive for whatever reason. Sometimes just walking barely off the edge of the pathway may cause them to pop off. Also it seems that flying above the crops destroys them.
I'm having exactly the same problem, some of the planted crops just pop off and the soil reverts to dirt. Here's a screenshot of my farm:
The marked spots are the ones that popped out several times already for no apparent reason, although it happens on other tiles from time to time, but always the corner onee, not the crossbreeding. The matron is stocked up and has energy. Also I made sure that under the farm there's dirt.
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