I used 10 nut peas on this guy, and it said the pet gained 18 total intelligence. 

http://beastkeeper.com/pet/100733

I had this quest with 62 intelligene. Of a pure black puma. Before I used any food on him he had 47 intelligence and I only need to up his stats 15 points.  Well his stats were supposedly upped 18 but, his intelligence isn't 65. It isn't even enough for the quest. What is wrong? I do know that he has the dominant gene silly, but I do not think that matters.

It is like its only counting for some points and them some e counted as a negative/neutral Stat. I know for sure he didnt have -55(not 100% that is how much) intelligence because of silly or any other gene. I remember him having -46 before I used some of the nut peas.

I'm pretty sure the silly gene DOES matter here. It decreases your pet's base intelligence stat by 50% and as Magic Food increases the base stat as well you only get half of the value because of the gene.

So your pet in fact gained 18 intelligence but it's silliness took away 9 (that's also why you have -55 now and not -46).

Everything seems fine to me here..

drak is right, magic food affects the base stat value.