Hi @Manuss_Ponce,
Others have reported similar issues:
I am not sure where this is coming from — 16S rRNA gene primers probably should not be amplifying chromosomal DNA from a mouse, but depending on what primers you are using I suppose it is possible. I wonder if cross-contamination could be at fault (e.g., from other experiments of RNAseq preps of mouse DNA?)... but first thing you should do is check your primers. Next talk to your sequencing facility...