Hi Narwhalsarefalling!
Thanks for sharing your experience. Unfortunately in this game time doesn't stop, it keeps going whether you're at the computer or not. This is by design, however can see this might come as a surprise if you're not aware.
If something like this happens, you can press f12. This will delete the local save data, so you can essentially start from scratch.
Hope this helps, though glad to see you're enjoying it anyway :)