So, I'm also playing on firefox as a browser and I seem to have the opposite issue: sometimes the drill inventory gets stuck on empty and doesn't fill up anymore unless I click 'collect' on the empty drill. Kind of seems related, so there might be an issue there.
However, good news: unless you're desperately waiting for your first scraps of iron ore, active clicking seems to vastly outperform the machine collecting and the machines are only useful for increasing the passive stone mining in the current version. That's why I fill all slots with drills, because they seem to boost passive mining more than the other types. Once you got the stone rolling from passive and active mining, trading ores for stone and basalt also seem to be solid options. Much better than the machines at least.