Why does some coffee smell like urine?
This answer is purely speculative in nature fueled by high school science and a research paper    

From medicalnewstoday


  Urine does not usually have a strong odor to. However, occasionally, it will have a pungent smell of ammonia.  


Googling coffee + ammonia led me to this little article Filter coffee nanoparticles to turn ammonia sensors.  

The article  says that the researchers at IISC Bangalore were using coffee powder for detecting ammonia because coffee powder contains carbon and nitrogen in abundance and they've used that to make carbon nanotubes whatnot.  

Then I hit gold when I found the research paper itself
- Understanding the ammonia sensing behavior of filter coffee powder derived N-doped carbon nanoparticles using the Freundlich-like isotherm. 

The detecting technology is based upon adsorption which is a surface phenomenon basically the adsorbate(ammonia) gets concentrated only at the surface of the adsorbant(coffee powder).   

Now, there are two types of adsorbtion. 


Chemisorption  
Physisorption 


Now comes the speculation I'm assuming that the process over here is physisorption because physisorption is inversely proportional to temperature.  

How it works?. 

Filter coffee is essentially a powder this provides a large surface area for adsorbtion.

Intially when the coffee in your kitchen at room temperature some amount of ammonia gets adsorbed on it. Now, when you make the coffee it is exposed to high temperatures and as you can recall I just discussed that in physisorption the amount of gas adsorped on the surface is inversely proportional to temperature so the hot coffee can hold less amounts of ammonia on its surface as compared to the room temperature coffee.   

So that's how ammonia is released on making coffee. Presumably.