Disarrange
/ˌdɪsəˈreɪndʒ/
Definition 1 of 1
Pro Tip 1/3Negative Connotation
The word 'disarrange' often implies something negative, as if things should not have been disturbed. 
He was annoyed to find his tools had been disarranged.
Pro Tip 2/3Physical Spaces
Commonly used for physical objects or spaces that have been made untidy or out of order. 
The storm disarranged the furniture in the garden.
Pro Tip 3/3Unintentional Action
Sometimes 'disarrange' can suggest the action was accidental, not done on purpose. 
I didn't mean to disarrange your documents.