I am reviewing a software library tool at the moment. During the review, I found some minor bugs while running their examples. However, it seems like nobody else has these bugs (at least I cant find them on the Github issue page). Otherwise, the library seems to be great. Should I recommend an accept pointing to these bugs or post the issues on Github (which could technically reveal my identity though, which would be against the blind review process).
You should submit the bugs with your review, not through Github.
If those bugs and bug-fixes are critical to your review, you should submit it with it and don't make a pull request from your official GitHub account. You still have an option of creating a one-time account and point to those issues/submit pull request fixing them in GitHub – that will not reveal your identity.
If your review does not really need those bugs to be mentioned (they are tangent to the subject of the review and don't influence the evaluation much), you can omit them from the review and post them officially through GitHub. That still has some possibility of identity reveal if the bugs are very special, and there are very few (say, 2) reviewers that participate in the peer-review process.