Want to farm Holy Stones? Just go to some easy area (eg. Asdivine), double the encounter rate (or, if you have the resources, anything which grants 1 encounter per step), set difficulty to easy, and Battle Shortcut to ON.
...or off. I can't remember.
Just wander aimlessy, but really, if you want to to get covered with Holy Stones, just use twitter. So easy. Just, uh, don't go messing with phone date to twitter from 01-01-1970 until today. Eh, that's stealing! Also, you're violating the EULA which
everyone reads and totally cares about, right? right?!
But really, I installed the freemium a few weeks ago, and I am only really playing today. What I did on the previous weeks? Twitter! :Þ
Now I have around 200 Holy Stones to... I don't know. I can't decide what to use them on!

So many choices...
On side note, instead of “Holy Stone Problem” try a more descriptive title like “How to farm Holy Stones?”, thanks in advance.