how confident we are if a read aligned to 23S belong to the bacteria of interest and not other bacteria in the same region that are in our sample?

I have a somewhat maybe naive question here, my background is statistics and recently I entered Bioinformatics world and I enjoy every second of learning all about it. So my question is related to alignment:

I have a sample of different bacteria and I aligned it using bwa mem tool to bacteria references. I am interested in finding a mutation in a universal gene, say 23S or 16S in a specific bacteria, say gonorrhoeae. How confident we are on the result of the alignment? what if a read that aligned to 23S in gonorrhoeae genome comes from 23S of another bacteria and randomly placed in that region for gonorrhoeae. Is such scenario possible? is there a way to avoid or at least minimize this issue?

Thanks