The problem here seems to be that your were travelling on separate tickets, ie one ticket for UA between EWR and BOM and a separate domestic ticket for 9W between BOM and IDR.
Each ticket forms a separate contract with the airline so as far as 9W is concerned you were not making an international to domestic connection. Rather, you were taking only a simple flight between two domestic points.
Was there a particular reason why you did not fly 9W throughout between EWR and IDR ? I ask, because 9W’s website does quote a through fare for this route.
As for your domestic ticket showing 20 kgs … well that’s either a mistake or your ticket could have been issued before 9W reduced its domestic checked baggage allowance to 15 kgs only a fortnight ago.
If it were the latter, one would think that 9W would honour the 20 kgs allowance.