I think the major issue is pune junction. Being a big city it has only 6 platforms out of which only platform 1 is capable of handling 23/24 coach trains. Rest are not that long. And many a times due to platform unavailability trains have to halt for long time at outer. This is also perhaps one reason for South bound trains getting diesel-powered locos from Mumbai itself in order to avoid Loco change time at pune junction. Perhaps some senior members can correct me if i am wrong and throw more light on it.