I don't know what happened, I've been using the console in html games without issue, but suddenly today I tried to use it and I keep getting an intrusive pop-up that won't let me doing anything until I click ok.
It isn't a full fix, but I answered another post about this. It does this on Chrome and Chromium Edge Beta, but it seems to work fine with the regular Chromium Edge. I'm guess some code was added/changed somewhere that's a causing a conflict with the way Sugarcube outputs its file.