If all three samples contained a total of 15,000 events, then any difference in the hight of the peaks comes down to 1) any upstream gating strategies that you may not be showing me that affect the three groups differently or 2) the distribution of staining is different for the groups resulting in different histograms. From what you show me the latter is a clear contributor. You see many more red events on the left side of the plot that is reducing the count of cells in the main histogram peak. Maybe they didn't get stained (uptake the dye) or maybe they are dead cells or debris. Cell viability dyes and light scatter gating may help in selecting viable cell populations to compare.

I would only add to the detailed and precise comment above that it is clear to me the red population is more spread around to the X axis (wider base), meaning that the staining efficacy is somehow impaired in this cell population. Go for viability dyes and always do SSC-FSC at least. Good luck!

Thanks Marcus and Damiano for your kind response. I haven't gated any of the cell lines results, but I checked the SSC-FSC plots and noticed that the red cell line has more dead cells or debris compared to others.