Should one be especially conscious of removing low counts, when applying batch correction?
I don't think this has anything to do with batch correction.
The averages of that gene are distinctly different between groups, so it's correct that the gene is statistically significant.  But with one sample driving all the difference, it's likely to be an artifact, or otherwise not fruitful to follow up on.
As geek_y suggested, a filter like &quot;omit genes unless 2 samples have &gt; 10 counts&quot; would drop that gene.