Try removing this line
import mypackage.Array;
so you do not import this custom Array and you always use the fully qualified name, I did not tested it but this should fix it.
EDIT: I tested this and yes you have to add this import line, it will not work , but I can't reproduce the error, I can use and custom Array and the global Array fine with no issue/error or warrning.
EDIT2: This also worked for me, can you test this too?
var globalArray:Class=(getDefinitionByName('Array') as Class);
var arr2:*=new globalArray();
arr2.push("test");
trace(arr2);