I have an ongoing issue with pop-ups running off the edge of maps when the map is embedded in a website . In this particular case, it is a web map (Classic) embedded in an Experience Builder scrolling page. When you click on some locations, the pop-up is cut off by the edge of the map. Here is a screen shot (the data is not approved for public consumption, so I had to black it out).
Screenshot of pop-up running off the edge of an embedded map.
As an alternative, I tried to turn off pop-ups in Experience Builder and use the Feature Info widget instead. To get the Feature Info widget to filter, you have to enable the Selection tool in the map. That's not a problem per se, but there is no way to automatically activate that tool. The user has to know to click on the select tool first to activate it. Further, when you make a selection (even with the point selection tool), you don't get one location. You get the location you clicked, plus everything within an unspecified buffer. So, it's really not a good alternative to the in-map pop-up.
I've had this same problem when embedding web maps and web maps inside Civics Plus web pages and found no solution. I could potentially convert this particular project to Experience Builder Developer Edition and try to tinker with the source code, but I have to believe that I'm not the first person to experience this issue!