The auto-clicker is a bit odd when it comes to the upgrades, particularly in the web version, yea. I think it requires a little bit of manual clicking on them before they'll start working properly, but I'm not entirely certain why it happens, though I'm probably gonna rework the thing entirely to work more consistently across the board since it's had issues for a while. Thanks for playing!
Also, the ending scenes went by fast due to having the autoclicker on, I kinda didn't think of that, I should probably force-disable it during that since you progress the scenes manually by clicking!