I think in draw you need nested for loop, to check each bubble against every other bubble:
for (int indices = 0; indices < bubbles.length-1; indices += 1) {
for (int indices2 = indices ; indices2 < bubbles.length; indices2 += 1) {
if (bubbles [indices].together (bubbles [indices2])) {
bubbles[indices].pops ();
bubbles[indices2].pops ();
}
}
}