Rather expensive and inconvenient lesson for you, but surely you learn something everyday

I'm not sure on what terms of use are US emergency replacement passport, but ours (Indonesian equivalent of that) is surely can only be used once. One way til the final destination. Once it's used, we shall get new passport in overseas embassy / overseas consulate / home immigration office.

I'm guessing you requested the "taxi" via Go-Jek apps. Grab clear distinction on its app whether you'd like to hire motorbikes or cars.
Go-Jek automatically selects bike, while if you wanted car go for Go-Car. Go-Bluebird for metered taxi.

Note: Nyepi is not Indonesian new year exactly, it is specific new year only for the Balinese Hindu.

As for denied entry, I think it won't be an issue unless you need to apply for advanced visa. If so, clearly mention that you're denied entry because of the emergency replacement passport. It's not a dodgy thing, it's just a mistake that some people made.