Basically, it is a contract issue.
Contracts are instruments of choice for dealing with uncertainty.
It may be too simple an answer for a farmer to check the label and stick with non-genetically modified hybrids. At the moment, it appears that seed companies are not in a position to warrant that non-GMO seed is GMO free. Seed companies concede that contamination, particularly from pollination, can occur and likely does occur but at a fairly low level. Some estimate the contamination at less than one-tenth of one percent. The problem is that no tolerances have been set for GMO germ plasm in non-GMO seed.