org-toggle-tag always marks the buffer as modified due to how it is implemented. It would be better if it did not mark the buffer modified if it does not change anything. This is annoying for org-depend.el (which is contrib, not officially supported) because the org-blocker-hook set by org-depend.el will mark the buffer modified whenever an agenda view is built/refreshed.
Glancing at org-toggle-tag, the feature isn't difficult to implement, but it'll be ugly. Emacs : GNU Emacs 26.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.22.24), modified by Debian Package: Org mode version 9.1.13 (9.1.13-elpaplus @ /usr/local/google/home/ayatane/.emacs.d/elpa/org-plus-contrib-20180618/)