So, I was a little surprised when our vet told us about the crystals. She continued to say that when cats develop crystals in their urine that they will urinate outside their box to tell you that there is a problem. So I feel bad that she might have been trying to tell us something all this time. However, in our case, I still think it was a little bit from column A and little bit from column B.

Apparently, the problem is easier to detect in male cats, since instead of urinating in odd places like females, the male cat actually becomes unable to urinate. More about that here. Perhaps using Comfort Zone would help.