I’ve experienced a similar thing at the local pool/snooker hall. Not with Apple Pay, but I’m sure it makes little difference.
Slightly different though, I got the notification on Monzo that the transaction had gone through, but the owner accidentally hit the cancel button on the terminal before it fully completed.
Obviously I told him it appears to have gone through but was happy to go with whatever his receipt said (cancelled) on the assumption that, like most banks, it would reconcile in 3-5 working days.
To my surprise, before the second transaction went through, the first refunded.
So, I believe, it’s just a side effect of the awesomeness of Monzo.
Not sure why it declined on your side the first time, but the whole auth/reconcile/refund process is definitely a refreshing change from legacy banks.
I remember back in the day something similar happening to me in Tesco. Money was certainly not abundant for me at the time and I effectively lost £40 out of my account for the best part of a week. Tesco couldn’t help, NatWest couldn’t help, I just had to wait.