The problem is that you recycle the data list.
When you do Vertexgroup v=new Vertexgroup(idname, coordx, data); you pass the data as parameter. Like all parameters in Java, it is passed by value, but the value here is just the reference of the list. So when you do data=_data; in the constructor, the new instance has only a reference, a kind of pointer, to the list.
Then you clear the list, deleting all data you added to it, resetting the values for all the instances referencing it, and you fill it with new values, again shared by all instances...
A better way would be:

1. void prepareVG() {
2.   int idlocalprev=0;
3.   ArrayList<Float> data = new ArrayList<Float>();
4.   
5.   if ( db.connect() ) {
6.     db.query("SELECT * FROM base_cartography LIMIT 2000");
7.     while (db.next()) {
8.       
9.       String idname = db.getString("idname");
10.       float coordx = db.getFloat("coordx");
11.       int idlocal = db.getInt("idlocal");
12. 
    
13.       data.add(coordx);
14.     
15.       if(idlocal<=idlocalprev){
16.         Vertexgroup v = new Vertexgroup(idname, coordx, data);
17.         vgList = (Vertexgroup[]) append(vgList, v);
18.         data = new ArrayList<Float>(); // Create a brand new list
    
19.       }
20.       idlocalprev = idlocal;
21.     }
22.   }
23.   db.close();
24. }

About the line vgList = (Vertexgroup[]) append(vgList, v);
You can make it another an array list:
ArrayList<Vertexgroup> vgList = new ArrayList<Vertexgroup>();
then you can do:
vgList.add(v);

Note: I don't get why you pass the last coordx to Vertexgroup. It is redundant with the information in the data list. You could pass / store idlocal, instead. It depends on what you plan to do with the data, of course.