[BioC] DESeq variance question

[Steffen Priebe]

I was using DESeq (and edgeR) for differentially expression analysis. 
In my current dataset I compare 3 biological replicates of control vs. 3 biol. replicates from a mutant. 
The resulting 4 top genes according adjusted pvalue by DESeq and edgeR have a very high variance. 
(The reason for this is, that this are genes located on the chrY and only one replicate of the mutant was male) 

My question is now, how can genes with such a high variance of the counts result in this small pvalues? 
Is there any way to avoid this, because I think this are False Positives? 

Attached you can find the combined result table of DESeq and edgeR for the top 100 genes. 
The problem occurs for the first 4 genes. The raw counts are stated in columns P-U (P-R: Mutant, T-U Control). 


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