Why doesn't FindMarkers() evaluate all genes even when all thresholds are lowered?

[zrcjessica]

I have a large scRNA-seq from multiple samples, each representing one of two conditions. Within each cell type, I want to measure differential expression of genes between the two conditions. However, regardless of the test I use, even when I remove all of the prefiltering thresholds (logfc.threshold = 0, min.pct = 0), not all of the genes found in that subset of cells is evaluated for differential expression. I thought this was because some genes weren't detected in all cell types, but I poked around my data and that doesn't seem to be the case. Is there a reason for the fact that some genes don't get evaluated even without prefiltering thresholds?

Thanks