If i have understood your description correctly I think this is normal. The Y shape confused me, but I think you are talking about one drainage tube and the other tube which is used to inflate a balloon which keeps the catheter in place.
Also the tube down to the leg bag on mine was not corrugated, just a clear plastic tube.
Anyway the tube from the end of the catheter to the bag is always full of urine, this seeps in to the leg bag which you empty every so often but the tube never empties. I think the top of the leg bag has a one way valve to prevent flow back. I think if you get bubbles in the tube these would travel up the tube in to your bladder, and though this is probably not a problem, it isn't something your bladder would ever get naturally.
So in short don't worry about it, as long as the bag keeps filling up and you keep emptying it all should be OK.