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Why are my holdings not displayed in the exchange where I bought them?

The stocks in your demat account don't have any exchange mapped to them. You can sell them either on NSE or BSE, regardless of which exchange you bought the stocks. Your Kite holdings will reflect the exchange price where the previous closing was higher.

Ideally, the price on both exchanges should be the same, but sometimes there can be a price difference due to:
  1. A corporate action or IPO: Check this price difference on 15th June 2020 in Alok industries due to corporate action
  2. The difference in tick size: On BSE the tick size for some stocks is Rs 0.01 and on NSE it is Rs 0.05
Accordingly, if you decide to exit your holdings without checking the price on both exchanges, you are more likely to sell on the exchange where the price is higher. You should still check the price on both exchanges since this feature is based on the previous closing price as opposed to the live trading price.

In order to sell your holdings from the non-default exchange, you can add the stock to Kite Marketwatch and sell it.

You can check this BSE circular where SEBI now requires any constant exchange preference to be removed from the trading platforms and to show the best available market price across both the exchanges.