I just ran into this issue, and I was wondering if this was a organization security setting.
I am working in two AGOL accounts. One is my own that I administer, and I have no problems with the pop up URLs, they work as they should (i.e. I create a custom popup and specify an attribute as my website link, & voila! popup has a nice link to an outside URL that works fabulously).
The second AGOL account is for an organization and I am a user who can create web maps. But creating a popup with a custom website URL results in it appending the organizations portal URL to the beginning of whatever website I have in my attributes.
i.e. "www.google.com" in the attributes becomes "<organization>.maps.arcgis.com/home/webmap/www.google.com"
My only guess is that it is a security setting...
Since I do not administer the second account, they are asking what setting they need to fix in order for the popup URLS to work properly.
Anyone have any ideas?