Hi @Anonymous User ,
Thank you for your reply. Today, I don't see the issue anymore. I opened a case (#02955359) with Esri Support and can tell them that it is fixed.
But, the issue that I now notice is about the pop-up in the map (in configuration and after publish). When you click a visible feature, it will also show the info from the features that are hidden and the pop-up is therefore not in sync with the time slider. This is confusing for users when they want to have info about the visible features.
I will use this case to have Esri Support look into this.