Transgene silencing is a common phenomenon in case of plants. Transgene could be inserted anywhere in the genome, which might be either functional or non-functional areas.
Silencing of the transgene could occur either during transcriptional or post-transcriptional period through siRNA (Small interfering RNA). This might be because of the wrong expression of both the strands of the transgene inserted. The reason why even though EPSPS (enzyme in the shikimate pathway) gene is inserted, some of the plants were not resistant to the herbicide. This is because of the fact that the inserted transgene would be silenced through the siRNA that would interact with the transcript before or after processing of the transcript. Thus, enable the plant to be sensitive to EPSPS.