2007 Toyota Yaris

Recently there is a check engine light on the panel started. Once the light comes while shifting the gears there is a jerking sound. There is no problem with acceleration. Once the check engine light goes off, then there is no problem, no jerking sounds while shifting. I showed to the toyota service centre but they are asking to replace the whole system instead of identifying the problem. I recently changed the transmission oil but the filter changed around 25000km before. I showed to different mechanics but no body correctly told me where is the problem. I need your expert advice in this matter. Best Regards.