I found another bug, but this time its repeatable.
I don't know if this is the case an a save but starting a new game. get to the point of getting the supercomputer. select the recipe and load up tech cards to process, now at this point you should see the temp rise. now if you spend some time like that working out how to solve the simple math problem, you then look to get it right but nothing happens, then you see the building is over heated, now at that point i saw the heat output 100MW, well i dropped in 51 heat sinks to deal with it but it didn't cool off. i made a few more and ended up having to use 60 to get it cool off enough for it to crafts. now once you get your fist card made it starts to work like it should the heat dropping when not in use. I left the massive block of head sinks because i cant be asked.
I loaded up a new game with creative mod on and speed run to the super computer and setup a little test save if you want it. but i narrowed it down to some start up state between loading it up with cards but before you solve problems. it seems to be buffering the heat as in my game it took like 4 minutes before it cooled off enough to start running, then what ever thermal script you have running started working as it should.
No bug, this is just how it works. The machine consumes energy constantly while its crafting is in progress (which is any point after you initially generate the problem)
You can always shut off a supercomputer by circuit control like you can any other assembler. Or simply destroy and replace it.
ideally you should just build enough cooling to support it running constantly, which is what you did.