This one is relatively easy to answer – the hardest thing is when your experiments just dont work and you can not work out why. This can be really frustrating and requires you to stay motivated and keep thinking and reading about why this might be the case.
The hardest thing of a scientist working in a research and development environment is facing different types of challenges so often and therefore you need to be able to keep learning and creating new techniques to deal with new issues. Being a scientist is also a responsibility, because your findings will be relayed on by decision makers in the organisation where you work.
I would say that you have to face failure at a regular basis, either because the experiment was unsuccessful or your manuscript was rejected from a journal etc. So, you need to be patient and persistent to your goal and to your work.