first i would like to start by saying y is your 3 month old baby not receiving any breast milk.. and also how is the child being fed? is it with a spoon or palada?
coming to the reports you have mentioned it looks like an infection which is shown by the pus cells..
this infection may be interfering with the digestive process.. the food un digested is acted upon by the bacteria leading to production of foul smelling stools.. please visit your close by pediatrician
for a course of antibiotic and advice on feeding..
coming to the issue of weight there is nothing wrong with the growth.. a baby doubles its birth weight
around 4 -5 months.. what you need to remember is that rate of growth varies with age of the baby and cannot be measured on daily basis.. baby is appropriate for its age..