I have a Jekyll website that also uses paginate-v2. I was deploying it on GitHub pages, and it was working fine, until I added pagination.
You can get the code on https://github.com/divyessh/tennis-events/
And here is the last deployment without pagination:
I am also facing the same issue after some research I have a solution if GitHub pages do not support Paginate-V2, if you want to use that then you need to integrate with the third-party cms like I am using site leaf which will allows you to utilize the functionality in v2
https://github.com/DevlopersField/jekyll-paginate-v2
for more https://learn.siteleaf.com/themes/jekyll-plugins/