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At least in experimental physics a significant chunk of your time is taken up by menial duties. This might be babysitting the gas-detector or anything from server maintenance, PCB-design, ASIC development. Some of it can turn into your PhD thesis, a lot of it is just uninspired grunt-work you are expected to do. Of course you are also typically only paid ~65% of a full salary, so a significant chunk of your work is unpaid, because of course people expect you to work full-time. An alternative way of stating this is that you are expected to do your PhD research in the 35% of the unpaid time.

This is in principle illegal, but because the institutes don't have any automatic time-tracking, you are instead expected to lie on your time-sheets and to underreport the time you've worked.