Because the seeds weren't his own anymore. What, you think he believes he bred a roundup ready crop? That's why he lost the case, he definitely knew what he was doing.
How come the seeds aren't his own? The complete genetic structure of his seeds is certainly different to the Monsanto ones. It's just that the one allele got transferred via cross-pollination and remained in his own seeds he preserved, giving the seeds one specific property which is the same as in the Monsanto seeds.
Breeding is selecting your own seeds based on their properties, and Schmeiser was a breeder.