What Does It Mean When Cross Correlation Between Two Images Occur at Negative Coordinates
It means the best match to template happens outside the image.
For instance, let's say your template is 5 by 5.
And you got answer which is -1, -1. It means the part of the image which best matches you image is centered at [-1, -1] and you only have part of it in your image.
This is really an extreme case.
P. S.
If you share your data (2 Images) we'll be able to assist more.