I have long thought that GUIDS are unique, well GUID actually stands for Globally Unique Identifier. And SharePoint is one unique product using GUIDS everywhere. There are 2^128 possible GUIDs to choose from, so there should be no need to reuse GUIDs as long as I'm alive.
SharePoint uses GUIDs to uniquely identify Site Collections and Sites, and more, and this is, for instance, exposed through the ID property of the SPSite and SPWeb objects. If you take a look at the documentation for SPWeb.ID it actually says: The globally unique identifier for the website – which I interpret as this ID is unique, globally! Period.
When you create a Site Collection in SharePoint, you create a new Site Collection (SPSite) and a Root Web (SPWeb). The SPSite will be given a unique identifier, a GUID, and so is the root web as well. Due to the way the API is created, you cannot find a web directly using the unique Web Id, you actually need the Site Id. Even so, there are multiple applications and services that have only stored the unique Web Id and used that as something unique.
Given (recent) changes and a new feature called Fast Site Collection Creation, used in SharePoint Online and to some extent in SharePoint 2016, this is no longer true and you can no longer trust in the Web Id being unique. When a site collection is created with a root web, specifically the SharePoint Team Site (STS#0), it is copied from a site master. The Site Collection is given a new GUID, but the GUID for the root web is copied from the site master. So, in SharePoint Online all your Site Collections with a root site of type Team Site will have the same id.
There is no workaround for this, you cannot change the Id – your only chance is to use a combination of Site Collection Id and the Web Id. That is a dual GUID combo – can't be more unique than that.
Some of you perhaps already knew this, some not. Hopefully you'll be aware of it now and I wish this would be different and that the Fast Site Collection Creation actually updated the Site identifier property, and since I most likely cannot have that I wish the documentation would be updated with a hint on this.
You can find Wictor's original post, along with other great posts, here: When a GUID is not really unique - I'm looking at you SharePoint!