A different issue entirely with notifications, but the Redundant Department of Redundancy is working overtime.
Gift a race: You get a notice that you gifted them, followed by their accept/reject the gift. There is no need for the first notice as you just did the gifting.
Meet a Pirate: Sometimes it open the diplomacy window and offers Protection there. Other times it opens one to two message notifications of the Protection offer. If you accept both, do you pay twice?
An Empire offers you a treaty and you click accept, only to have them reject the treaty. I suspect that you Diplo level might have dropped in the time it took to click.
In later games, notifications can appear onscreen that have aged out of existence before being displayed. 4x is bad at that time.