Most important thing if you are shorting something with circuit filters make sure you cover it before the circuit limit is hit. You can avoid the whole process of auction. Check the nse, bse website daily for knowing the days circuit limits. If you are shorting pick something which is traded in the derivative side(Futures and Options). These stocks in the cash market have have no circuit limit. And above all think twice before shorting newly listed stocks you never know where the operator is taking the stock.Better safe than sorry.
Regards,