Did you apply orbit files before coregistration? You can increase the number of GCPs and change the window sizes. In general, the images which you want to co-register should not be too small so that a sufficient number of GPCs can be found throughout the image.
Otherwise, you can download the SLC products and use the S1 TOPSAR coregistration. It allows for the definition of sub-swaths and bursts and produces correct results most of the time.