Any nonstandard transaction will be rejected by 90 if not 100%, miners, but if you get lucky to get someone to mine it, it will work fine with the protocol.
The nonstandard txs are any that are something more than a transfer, multisig (i.e. the ones that have some sort of smart contract capability).
This is not theoretical - literally killed my project of decentralised oracles (Orisi) back in 2014. Our beta transactions were accepted only by 10% of miners, so you had to wait for hours to get your tx through. Perhaps it changed - I think in 2018 not even one mining pool accepted that, but perhaps by now they fixed it, although I doubt that.
May seem like a small thing, but I met other projects that bumped into it. They had the tech, just didn’t manage to convinve miners to accept their transactions.