Others have been experiencing the same thing.
Many My eBay pages have a "Tell us what you think" link in the upper right that can be used to alert page developers to issues such as this. If you do not see such a link on whichever page you experience that pop-up with, try the link on the Bids & Offers page:
https://www.ebay.com/srv/survey/a/myebay.bidsoffers2
You may be able to use an ad blocker's element hiding tool to temporarily block all notification popups on eBay, if you are using a desktop browser.
Most desktop ad blockers have a point and click interface to allow users to block certain page elements from displaying. With a little trial and error you may be able to block those notifications completely in one browser, then disable that ad blocking rule once eBay fixes things.
"We are not what we know but what we are willing to learn."
