Some species that the boundary conditions tag (BCON) tracks are reactive. When these encounter other sources, particularly those with highly concentrated emissions such as from a power plant, they will react. A fraction of the products of these reactions will be attributed to BCON, because BCON provided the reactants that created these products. This can be controlled by the user to some extent through runscript options for ISAM. There was a very recent webinar that explained this in more detail. Perhaps, someone can link it here for you.
I am not sure what you mean by your second question. ISAM tracks emissions streams, ICON, BCON, and potential vorticity at the top if you have that turned on. If you are tracking an emissions stream(s) that to provides precursors into any CMAQ module, these these will show up in your tagged species. If you don’t specify some emissions stream, it will be lumped into the OTH tag.
Sergey