Allele-specific bisulfite sequencing
I agree with Vance, we need a little more detail to better answer your question. From what I can tell, you are asking whether a single nucleotide polymorphism (SNP) that results in the addition of a cytosine base to your sequence is of concern when examining the methylation signature of that sequence. 

I would first determine whether the polymorphism is common in the population using NCBI. The more common the polymorphism, the less likely it is to have a serious effect. However, that is not to say that it doesn't have any effect.

I would then examine how much the methylation of that one site varies compared to samples without the additional cytosine base.

Finally I would determine the importance of the location of the SNP. Is it located in a CpG island? Or is it located on the shores, shelves or 'open sea'? (see work by Sandoval et al.)

Without knowing all the above it is hard to make a call on how important/unimportant the SNP is in your methylation analysis.