Hi
First I would like to say congrats for your effort to get transcripts (attestation format) from Mumbai University.
As per Rules, no one Colleges have rights to issues transcripts/attestation to Abroad credential service like WES/IQAS/ICES etc. Whichever university/institution are aggregated by UGC/AICTE/MHRD those institutions only have authority to issue transcripts. If you are college is an Autonomous then only your College can issue transcripts and it will be accepted by WES Canada.
But, in your case your College is a normal and affiliated to Mumbai University, hence please apply all documents at Churchgate campus, get attestation for all documents, courier to WES Canada once again and get an approval of your transcripts at credential service in Canada.