Maybe I misunderstood your post but that doesn't sound right to me. I always use the rear brake AND the front brake. That way if I'm in an emergency I can hit BOTH brakes without hesitation to minimize my braking distance and have a better feel for the limits of both. If I didn't always use both brakes, I bet I'd be more likely to under use or stomp on the rear !
You can still lock up the rear if you use the front brake. That will cause the rear to get loose.
You can also get the rear loose by using so much front that the rear becomes unweighted - it will float around if that is the case. Happens to me here and there on the track if I brake harder than normal for some reason - but easier to diagnose there as I know what is causing it...the rear end getting light from heavy front braking
Other factors come into play - suspension, grip of tires (function of pressure, temp, condition of tire), grip of surface, body position (how much you are weighting the F or R), etc.
It can also be (and likely is) attributed to a variety of factors working together, so very hard to say what the root cause is just by the description you gave.
Any way you cut it, the bike is giving you feedback - that the rear is losing traction. Harder part (since, like I said, we can't say "It was caused by X") is figuring out how to incorporate that feedback into your riding. But that is the normal maturation of a rider - figure out what the bike is telling you and figure out how to adjust your style to compensate...if you can do that, you are well on your way to becoming an accomplished rider.