The LastItemModifiedDate property of the site object in Office 365 reports the last time an item in the site was modified by either the system or a user. This causes a problem for anyone or any tool trying to do activity reporting to determine the last time a site was modified by a user. Please create a LastItemModifiedByUserDate and/or LastItemModifiedBySystemDate to allow us to distinguish the two.
This post says that Microsoft has fixed this problem: https://sharepoint.uservoice.com/forums/329214-sites-and-collaboration/suggestions/15112005-modified-dates-in-site-contents-should-reflect-con
This is also an issue with list and libraries. See:
This is critical for governance / control of aging sites. Reporting and 3rd party tools grossly undercount the number of sites not modified in the last 180 days. It is next to impossible to apply an enterprise policy to clean up sites that have stopped providing business value when the Last Modified information doesn't reflect end-user activity.