Soil moisture using a capacitive sensor - can cheap version of it contaminate soil
The PCB is normally covered with a chemically resistant solder mask, so under normal conditions it would not release anything into the soil.  

If the mask is damaged, then the resulting corrosion would release small amounts of copper and possibly tin (and lead if not RoHS compliant) however that portion of the board is not normally inserted into the soil (the probe would fail quickly in that situation).

If the soil destroys the mask you have much bigger problems than the probe materials (ie toxic organic solvents).  

It's doubtful that the FDA would be the involved, as soil is not considered a food nor a drug (unless you have pica).  The EPA perhaps, but on a practical level they're more concerned with industrial waste situations.