It's all in the mind. It's human nature to blame things on something else, rather than take ownership for one's actions.
Stuff can get shuffled around in a small recess, agreed, and that's why we need to be alert when doing things. Make a mental note of what went where; it isn't difficult. Moreover, the situation is unlikely to happen if the stuff that's moved around is set back in place at the earliest or if one knows exactly what is where. (Don't accuse me of having OCD; this is just a routine practice that makes living so much easier).
Similarly, if the contents spill out of a box, its best to stuff them right back into the box, or do so at the earliest. It prevents swelling tempers, panic attacks and the sudden rise in blood pressure. Haste makes waste!
A quick trick to staying organised is to label stuff. Folders and boxes can have labels with what's inside them. Alternatively tape a sheet of paper on the inside of the cupboard doors, corresponding with each shelf. List the items on this sheet and update it whenever necessary. All the stuff I have in the lofts, in my house is labelled. I don't have to rummage through stuff to locate something I need.
For the most part of my married life, I've lived out of boxes, waiting for suitable 'A type' government accommodation. I learned this clever trick to number huge wooden crates and stick a list of what's inside them, on the inside of the lid. Additionally, I maintained a diary, with exact details. The first transfer was difficult, subsequent transfers were much easier, as I knew what went into which box. It made packing and unpacking and settling down so much easier.
"A love affair with knowledge will never end in heartbreak" - Michael Garrett Marino