We know that the genetic code is universal. My query is why the mitochondrial genetic code is different from universal genetic code?
Your premise is incorrect, the genetic code is NOT universal. There is a 'standard' genetic code, which is found among higher animals and plants and most bacteria, but there is a variety of other genetic codes found in the main genome of more obscure organisms. These are listed at: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi .
There is also no mitochondrial genetic code but a variety of mitochondrial (and plastid) genetic codes. One feature of genomes with non-standard genetic codes is small size, so that the number of proteins influenced by a change from a common precursor genetic code would have been small.
In the case of mammalian mitochondria there are fewer tRNAs and these have non-standard anticodon-codon interactions. Thus rationalization of these genetic codes may have been due to pressure to reduce the size of the genome.