Better late than never. I had the same issue while trying to update my docker image using the provided guide Passbolt Help | Update for docker container
My solution is as simple as it gets… the guide mentions
$ docker-compose up -d
With my installed docker version the command has changed to
$ docker compose up -d
so no dash between docker and compose. I dont know if this is specific to the operating system or there are multiple versions of docker clients available.
Just leaving this here because this was my first result showing up when searching for the error 
and the view count suggests that i am by far not the only one
Edit: Ok Docker Compose V2 got rid of the dash:
Docker Compose overview | Docker Docs.
I think the Documentation for Passbolt should be updated accordingly. When we are using a Password-Manager solution we should also use the up-to-date versions of our software