rotting stone?

It was labeled something like 'dead coral' or something at the store, asked several people before hand as well if I should worry about curing since it was so porous, was advised not too... But, after 1.5 months of nitrite and ammonia spikes, I thought the sand/tank was just super dirty with particulates, but then I pick up this rock, and there's a huge black section on the opposite side on the bottom edge. I'm pretty sure that was NOT there before... As far as I can tell it's the rock itself? Some parts of it appear as a calcified section, kinda like a geode, but any idea if this is the source of my never ending spikes? I took it out for the mean time, but ... uhh... ya... if you notice the chunks I broke off while I was examining it, are definately NOT the bright yellow color the rest of the stone is. If rocks are calcium based do they turn black in saltwater as they breakdown? The first thought I had when I saw it was, 'dam, it's rotting?'

 

The tank is only 3-4 months old (after cycle), only 1-2" of sand...
I was thinking earlier though it was about the time I put it in the tank that I started to see some spikes here and there, but as of late they just wouldn't go away...
But really, when I got the rock it was as you see in the pic, an overall yellow, but when I pulled it out, the edge was just black. Looked like some vegetable rotting, where you have normal color, then a black spot..
I suppose it makes sense, but I never figured there would be something organic mixed into a calcified rock.. I spose it's possible. Lesson learned