Issue regarding the overestimation of size

[jawad9-11]

Hello Sir, i have a question as you mention in the documentation of this software like low allele depth can also demonstrate that size of long allele has been overestimated. I attached the image as it also has low allele depth.

chr16-5731069-5731094 5/25 30.07/2.63
and there are 78 samples from 2183 showing this trend. Can You tell me how to deal with it?