If you are travelling Pune to Mumbai then your route will be Pune-Lonavala-Karjat-Kalyan-Thane-Mumbai. (Rake reversal required at Kalyan for Nasik side, which is not possible in Busy Stations like Kalyan.)
But if you are travelling to Pune to Nasik via Kalyan then route must be Pune-Lonavla-Karjat-Panvel-Kalyan-Nasik.
Kindly Check Intermediate Station of Pune - Bhusaval express.