There are many possible causes.
Use of a sample in an amount more than a particular value does not lead to increase, but leads to decrease of the yield. Reduce the sample amount. In the case of a cell sample, use it at a concentration of 1×106 cells/200 µL or less, while in the case of a tissue sample, use it at a concentration of 10 mg or less/150 µL.
Agitation or homogenization of the sample may be insufficient. Extraction treatment in the state where solid matters remain in the solution because of insufficient homogenization may cause tip clogging during extraction operation, leading to decrease of the yield.
Some tissues contain many muscle fibers and thus, make sure to conduct homogenization operation sufficiently.
Tap or shake the reagent cartridge gently, when the cartridge reagent contains air bubbles or when there is deposition of reagents or water droplets in the reagent-sealing region or in the upper region of internal cartridge well. Processing with residual air bubbles may prohibit complete aspirating of the reagent and cause, for example, foaming during agitation, which often results in deterioration of the yield.