Here are two suggestions. First, under the "Quality Control" tab, look into the "Missing Subsets" metric. It will point out any samples that are missing a major compartment (such as T cells), which often indicates missing markers. To explicitly look for staining issues, go to the "AOF" tab. The AOF (Average Overlap Frequency) is an efficient metric to evaluate and quantify the robustness of staining in flow and mass cytometry data (see Amir et al., 2018).
Learn more in the following video: