I assume that you have isolated genomic DNA, and have produced PCR product using this DNA. A PCR product will not methylated, even if the genomic DNA is methylated, because you do not have any methylases in your PCR reaction mixture. If you use Hpy99I on genomic DNA, it will not cut the site where CpG methylation occurs. However, in your case, the reason why your PCR product is not digested by Hpy99I is possibly because of a mutation in the restriction site in the genomic DNA. When you amplify this region by PCR, the mutation carries over and the restriction enzyme cannot recognize it.

Thanks professor Raj Aravalli for your response. I'm still confused in one point.

I have read about the amplification of methylated DNA, I understand that their is a completely different protocol for its amplification. Therefore, I assume that the regular protocol to amplify non methylated DNA  couldn't amplify methylated one.