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In one scRNA-seq sample I encountered the genes: Hbb-bs, Hba-a1 and Hba-a2. These genes appear on top of the list of the highest expressed genes but the 75% percentile of cells have very low counts. Therefore the expression is highly skewed.

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Reading from gene cards, they appear to be coding hemoglobin subunits and involved in oxygen transport. I think they may need to be removed before normalization, also because the analysis I'm running does not consider oxygen transport.

Has anyone encountered this situation and what do I do?

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You probably have red blood cell contamination. It's probably better to identify which cells they are. They'll probably cluster away from the cells you are interested in.

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They may be B cells, did you analysis if they have b cell marker?

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