That's odd. Thinking out loud:
1: Something in the prints washes out in the HCA bath, turning it brown.
2: Something in the water itself turns brown.
3: Something in the HCA makes the water turn brown.
AFAIK HCA is really just sodium sulfite, and I don't really see any way in which that would turn brown in solution. Leaving 1 & 2, with #1 being the IMO somewhat more likely cause. Can you describe how you process your prints? What developer do you use? Fresh fixer or reused (does the problem also occur with fresh fix)?