I doubt very much whether the small amount of harissa on the bones would make much difference to the stock. I use leftover bones too, and it's always been ok.
As a matter of interest, what do you put in your stock when you make it? I make different types of stock, mainly chicken and beef.
For the chicken, I use fresh raw hind quarters of chicken, unpeeled golden onions (about 1lb), a couple of carrots, about two sticks of celery, bay leaf, thyme and parsley stalks, salt added at the end of cooking . I simmer it for about three hours, the dog gets the chicken meat along with his crunchies,
I strain the stock and freeze it ready for use.
I make beef stock with 2 - 3 lb beef marrow bones,marrow included, which I roast in a hot oven for a couple of hours, then fill the stockpot with the usual sticks of celery, carrots, onions with skin on, herbs etc, and cook over a gentle heat for 3 - 4 hours with a good piece of beef on the bone, then strain off all the solids, give the meat to the dog (no fat), and freeze the liquid in convenient quantities.
Enough is never as good as a feast Oscar Wilde