A bug was introduced into a recent version of the Mapbox tool around draggable markers. If you give your draggable marker an ID with a single integer, when you remove that draggable marker, it removes all markers. Here is a video
That is certainly frustrating for sure. I am not sure why it is doing that. Can you reach out to the plugin developer so they are aware and maybe they can fix that for you? Sometimes the plugin developers are really good about updating a plugin, especially if it is a paid plugin. Which plugin are you using?
I also recommend using the ‘Step by Step’ debugger tool to check and make sure no other workflows are running that might conflict for some reason.
Hope that helps a bit. 
BDK is always great about responding and updating their MapBox plugin. Hopefully they’ll see this.