It’s all in the timing.

[EnoughIsEnough]

I’ve noticed that the timing in the game does not match the real clock. Try it for yourself, set something to create say two hours. Now set on your smart phone, pc, or just watching the clock for two hours. I’ll bet a buck the game will still be a few minutes when your timer reaches zero.

[EllunaHellen]

Yes, I think this has to do with jumping between farms or farm/town/fishing. Like the loading screens add up to that time I think.

[CottonTail]

Yes, it's the same with Tom (I find there are usually a few minutes added on to his two-hour naps) and when you build a new machine.