how to solve the phase shift of a ne555 timer
Is there any way to remove the wave before 2 ms or is there anyway to make it same as the rest in the graph.

Yes. First, you remove your NE555 from your design approach. It doesn't help you in any way I can think of when trying to convert a sine wave to an impulse comb.
Then, you remove the 741. It doesn't help you in any way when trying to convert a sine wave to an impulse comb, unless you have a large bipolar power supply, which you don't seem to have. Even then, it would be the least sensible opamp to use – many, many other opamps would be better.