Is short-selling shares in a SMSF allowed or not allowed? What about if it happened accidentally one time?
Yes it is allowed if it part of your over all strategy there is no such thing as accident short sell, you got to have short facility setup or account setup that can short either via CFDs or other means a normal buying and selling account you cant use that to short stocks, if you sell stocks you don't have in a normal share account it wont let you.
Some short selling is prohibited by SIS Act provisions which do not allow the assets of the fund to be loaned, used as security or subject to recourse or pledged etc. The sole purpose test also may need to be considered if external parties are related etc. As an investment strategy it may be permitted but the above concerns override what is seemingly permitted. Each instance may require legal advice. CFD and some complex / leveraged investments may require a complex risk management statement / process / policy. Many auditors may qualify for leveraged risk without it.