Penalties, as far as I was involved in vendor discussions, are a part of the negotiation only when the software provider does any work on the client's premises and are liable to that extent.
For software, you don't pay penalties that it might malfunction once in a while, that's what bug-fixes are for and you get offered an SLA for that, but only for response time, not actual bug fixing. Where you do get penalties and maybe even your money back, is when the software is listed as being able to do X,Y,Z and it only does X and Z and the contract says it must do everything it said it does.
For software, you don't pay penalties that it might malfunction once in a while, that's what bug-fixes are for and you get offered an SLA for that, but only for response time, not actual bug fixing. Where you do get penalties and maybe even your money back, is when the software is listed as being able to do X,Y,Z and it only does X and Z and the contract says it must do everything it said it does.