If the array is initially allocated by Array.newInstance(), those allocations are not tracked. Once the array is allocated by ordinary new A[1] expression, subsequect allocation via Array.newInstance() are tracked. See simple test case below:

package allocref;
import java.lang.reflect.Array;

public class Allocref {

    public static void main(String[] args) {
        Allocref r = new Allocref();    
        r.test();
    }

    private void test() {
        for (int i=0; i<100; i++) {
            Allocref[] arr = (Allocref[]) Array.newInstance(Allocref.class, 1);
            arr[0] = new Allocref();
        }
    } 
}

in this example allocref.Allocref[] instances are not tracked. If the test case is changed to:

package allocref;
import java.lang.reflect.Array;

public class Allocref {

    public static void main(String[] args) {
        Allocref r = new Allocref();
        
        r.test();
    }

    private void test() {
        Allocref[] a = new Allocref[1000];
        for (int i=0; i<100; i++) {
            Allocref[] arr = (Allocref[]) Array.newInstance(Allocref.class, 1);
            arr[0] = new Allocref();
        }
    }
    
}

[note the change in the first line of the test() method]. Everything works fine and allocref.Allocref[] instances are tracked by profiler.