After doing a web search, most of the seasonal references to Goa during the "off season" months (which are the monsoon months) are discussing the heavy waves and more constant and stronger on-shore wind. Coupled with the rains of the monsoon and the normal oceanic issues (rip tide, etc) and the ocean is usually marked off limits.
While some (younger) tourists would like the waves, most don't go to the beach to fight the waves, but to soak up the sun. During monsoon, there will be more overcast days. Also, if you are out in the waves and a monsoon squall comes roaring through, you might literally be unable to see the shoreline. Not a good time to lose your sense of direction.
Finally, as far as swimming goes; when the winds are calm(er) the ocean is going to be clear(er) and if you are snorkeling or swimming and can see the bottom slopes and the sun's position, you can tell your direction of swim more easily. if the water is churned up by winds, waves AND tides, you can't see much at all. At these times, losing one's sense of direction is more enhanced and ending up too far out is far easier to do. As it is also the off-season, there are unlikely to be (as many) lifeguards watching for the unwary tourist, so the beaches would be marked with swimming off limits or unsafe.
As far as bacteria goes, there isn't more sewage 'being dumped' during those months, but when the prevailing winds are strongly on-shore, what bacteria there is (along with all of the other debris of the ocean) will be pushed in towards shore, instead of with the Southerly currents, so yes, the measurable amounts of bacteria will also rise.