Why is my yogurt sour at the top and non-sour at the bottom
There could be a few things that are going on here. 

My best guess from what you have said would be the temperature or mixing is a little off. 

Let the mixture cool a little more before combining with the yoghurt. Also, do this gradually, adding a small part of the cooled milk to the yoghurt each time, mixing until smooth.

Hopefully, this helps.