Hello Nithin,
If you use dedicated options, mass balance should be conserved. E.g. use a distributive scheme for tracers (default = 1 in the 3rd item of TYPE OF ADVECTION or for SCHEME FOR ADVECTION OF TRACERS, i.e. characteristics which are not conservative), decrease accuracies (e.g. 1.E-8 or less), no use of masking...
Running the test case t2d_waq2d_micropol.cas seems OK to me with the (not so good) choices used to check this mass balance criterion.
As suggested in the rules, you can upload your steering files.
Hope this helps,
Chi-Tuan