Genes are removed either because the well filter, or if there were too few values for differential expression analysis.
The well filter on the Normalization page is determined by the “Filter wells” drop-down menu for removing QC wells and for automatically detecting likely outlier measurements (see a screenshot below).
The low replicates filter: ANOVA and Kruskal Wallis do not work with less than three replicates per condition, and so genes with two or fewer replicates for any experimental condition are removed. This issue is not encountered if missing values are imputed. You can see which genes are removed using the processing summary table.