I wish it were not the case. The present condition has nothing to do with the difference between JEE and GATE exam. It has to do with the difference in teaching approach towards B.Tech and M.Tech.
B.Tech.: It is assumed that you don't know anything. So everybody starts with a clean slate. You are taught basic Maths, Science and Engineering, along with humanities.
M.Tech.: It is assumed that you already know what B.Tech. students are taught in IITs. Even if the teaching standards in IITs are somewhat bad, the condition in other colleges is deplorable. There are no classes and even if there are, they focus more on memorization rather than understanding. In my opinion, the syllabus of M.Tech. should be simplified where students are taught more basics rather than advanced topics and then they will do well and the gap can be closed. We should understand the background of M.Tech. students and teach accordingly and not say that they have B.Tech., they should already know this. In an ideal world, that would be the case. But, we should look at ground realities and adapt accordingly.
When the foundation is poor, the building can never be strong.