There’s a number of reasons that could cause the bones to darken in pigment; metabolic bone diseases, metastatic (cancer) disease, use of minocycline (unlikely if you think it likely the cat was a stray), ochronosis, vitamin deficiency (especially vitamin D as it is required for the use of calcium and phosphorus), nuritional osteopathy, kidney disease.
Poison is probably not as likely a suspect, I’ve read a few papers (none specially on cats though) where poisons like rat poison can cause discolouration of bones. But typically this only happens over long exposure.
Congenital erythropoietic porphyria is also a possible cause. In the 4 years I’ve been at this shelter, we’ve seen 3 cases in kittens, which is not many when you consider the literal thousands of kittens we get in each year.
That could be very likely considering the dead cat anon found was under 6 months.
Are you certain the bones are actually dark? Could they be stained by something?
Do you have pics, anon? I, for one, am curious.