Hey @virk_rana
does your data stack contain scenes from before March 2015? In this case you still need to perform the EAP correction on your data. The automatic EAP correction was introduced In March 2015, so for all scenes before this date, you still need to perform this manually. Here is the link to ESA’s newsfeed with this information:
Maybe this causes the difficulties with coregistration.
Maryse