I can confirm this a vanilla bug, first and foremost.

When first contacting a xenophile fallen empire, the communication pop up will occur twice. This is not a huge problem. But when they ask for the brainscans (fallen_empires_tasks.23) of the uploaded aliens from a certain event chain, this popup will also occur twice, one on top of the other.

It does not pop up twice when they ask for a pop.

I have no idea what might being causing this, but I figured I'd lodge a report with you. I realize you're on break, but I thought this might be useful to have on hand when you get back.