you cannot avoid this. in a sandbox game you have many "small" actions that are simple and easy to understand. once they are combined/chained you gain in complexity, and this is what allows the freedom of the "sandbox".
Imagine you may choose between A, B or C (actions with the environment/an item, or an interaction with another player). When you combine those elementary actions you can have AB or BA or ACCBA or ABCCBABCAC or whatever. Those strings can get extremely complex. The "sandbox" must allow for these to be done, otherwise it is not a sandbox anymore.
Players who cannot grasp the slight difference between AABAA and AABBA simply need to sit back and learn/explore more. If it was easy and simple like WoW you just need to click on the same icon 100 times and that's all.
So, if you have freedom you have complexity and thus all those situations.