@littleviolette - I too had this issue on Discourse 2.9.0.beta10. I use an advanced filter where I would filter certain types of content and then bulk append tags to that content.
I noticed that some tags would be working but others would not. It turns out that the ones that were not working were part of the Category → Tags Setting:
Having the tags there did not allow me to bulk append an advanced search, even if the tags I was trying to use were from that same category.