I used DESeq2 with the default settings, and of the roughly 30,000 genes, 16 of them yielded NA values for both the p-values and adjusted p-values. I assume this occurred as a result of DESeq2 detecting an outlier in these genes - is that correct? However, I am using 44 samples in the case group and 59 in the control groups, so my understanding is DESeq2 should have automatically replaced the outlier and should have computed p-values for me, rather than showing NA. What is going on here? Also, I'll note that all variables in my DESeq2 model are two-level factors. Thank you!

Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pvaluesNA