For those wondering why their commits aren't auto-linking to work items for some of their repositories - this is a feature you can turn on per repository:
Within Project Settings | Repositories navigate to the repository that isn't auto linking, and then under Settings enable "Commit mention linking" (and potentially "Commit mention work item resolution"):

You may find that this is disabled by default for Forks, whilst it's enabled by default for brand new repositories.
There is no way to automatically link branches to work items; unless you create the branch from the work item directly, using the "New Branch" button or "create a branch" link:


Note: This link only exists if there are no other Development links on the work item - you have to use the "Add Link" dialog after that.
There is an open ticket for that functionality: https://developercommunity.visualstudio.com/t/automatically-link-a-work-item-to-branches-when-co/809745