I am on Arch Linux and use anaconda-mode with company-anaconda (here is a minimal init.el with which I can replicate the issue). I have Python installed both at root level from the primary package manager (pacman) and locally through Anaconda ~/anaconda3.
When I use no environment, company works well giving me suggestions. On the other hand, when I do
conda-env-activate and switch to the base conda environment (or any other environment), company stops giving any suggestion. With
company-diag I see "Completions: none(error fetching)". I still get suggestions when running IPython in inferior mode, but I see that company uses company-capf as a backend in that case, as opposed to company-anaconda.
I am a noob with both Emacs and Anaconda, and have been trying to fix this for a while. My first thought was that company-anaconda could have been relying on some Python package not available in the conda environment which I am not aware of, thus falling back to the root installation for that specific package and causing issues, but I have no idea if that is a realistic explanation.