A common anti-pattern I saw at Amazon was for some team to need some functionality, see a package in the "live" version set that had it, and grab it without thinking about how that package's dependencies aligned with their application's. Teams also frequently used the wrong dependency type (runtime, build, test). Things will "work" if you declare a test dependency as a runtime dependency, but you are setting yourself up for unnecessary version conflicts down the road (you can have multiple versions of a package in your test dependency closure, but not your runtime dependency closure).
As for what I missed at the company with the monorepo there were two things: The first was that there was no way to deploy a version of the code that was exactly the same as what was in production plus some patch. The deployment system could only deploy the tip of the master branch, so if you needed to patch in prod you were going to bring with it all the other changes that had landed on the master branch, for better or for worse. There is no reason that a monorepo has to have this problem, though, it was a limitation of the deployment system.
The main thing I didn't like about the monorepo though was that it was next to impossible for me to track the changes that were relevant to me. In Brazil, every package is its own git repo and it's very straightforward to just list the git history of a package and see what has changed. In the monorepo 99% of the change in the git history were completely irrelevant. Also, twice they needed to rewrite the history of the entire repo to expunge some secret that had accidentally been committed years ago. All the hashes changed and it was very disruptive.
So what's good about Brazil is that it gives you the advantages of a monorepo without all the source code literally being in the same repo. It's also good because you can maintain multiple versions of the same package together and migrate different consuming apps separately. What's not so great about Brazil is that there is really a subtle art to factoring your software into packages and version sets and most times you get it wrong in a way that leads to seemingly unnecessary pain. The fact that you don't have to update all consumers together means that its really easy to just not update consumers and you pay the price for that eventually. There's another big pain point with Brazil which is that it was traditionally difficult to import open source software from open-source repositories (NPM, PyPy, Maven, etc.). This has gotten much better in recent years and there are efforts to improve it even more.
Compared to Gradle, Brazil is great because it lets you avoid thinking about a lot of smaller details. You declare a dependency on major version in the Config file and it'll grab the latest minor version from your versionset. A versionset is basically just a giant package-lock.json or cargo.lock file for all of your deps that is constantly updated in the CI/CD system. Since artifacts are deployed at a versionset level, you can always look up what specific version of a package is deployed anywhere. This means you don't have to think about minor versions 90% of the time, but when something breaks you can easily find it since the versionset interface is connected to the code browser. You can also easily ask "where does this package version exist" and see all the versionsets that are using a version of a package.
I think one of the other big things I miss about it is how well the tooling worked with multiple packages. Brazil had a concept of a "workspace". Normally if you're working with a package it pulls the deps from S3 or wherever. But if you wanted to work with multiple packages that depend on each other, you would run "brazil ws add package-foo-1.0" and it would clone that package to your workspace. Any other package in your workspace that depends on "package-foo-1.0" would now understand to use the local copy to build instead of pulling it remotely. This worked fairly seamlessly with the the Intellij Brazil plugin, making cross package refactoring pretty easy. Doing the same with gradle or npm requires manual work.
One of the biggest ways that brazil was misused was around handling of major versions. For context, only a single major version of a package is allowed to exist in a versionset at a time. If you tried to merge in a different major version of a package into your versionset, your pipeline would fail to build due to "Major version conflicts". One of the biggest sins was around bumping the major versions of the dependencies in a library without bumping the major version of that library at the same time. This would lead to many broken pipelines. Let's say you have a library Foo-1.0 with a bunch of users on other teams. You decide to bump up the Guava version from 25 to 29 and publish the new version of Foo-1.0. Anyone consuming Foo-1.0 would automatically pick up the new version of that lib because it's just a minor version change, however the merge would fail with a "major version conflict" because the major version of Guava they're using in their versionset is still 25. This means you would either have to pin that library back at a previous version, or bump your dependency on Guava in all of you packages to 29.
I think this last point really highlights the big difference between Bazel and Brazil. Bazel makes bumping versions a pain because you have to upgrade everything at the same time. However it also ensures that if there's a security issue with a lib, everyone is forced to upgrade at once. Brazil allows teams to adopt newer versions at their own paces, however you need a more complex CI/CD system, you have to deal with major version conflicts, and you have to deal with longer campaigns to upgrade libs with security issues. I think the two systems just have different tradeoffs, though the biggest advantage Bazel has is that it doesn't require the tight integration with a CI/CD system so it's easier to open source and operate.
This is not entirely true. A version set can have an arbitrary number of major versions of the same package. This is convenient if you have multiple applications feeding from the same upstream version set. You can add a new major version to the upstream version set and the applications can all switch over independently. This is of course how different applications can all consume from the "live" VS which has multiple major versions of many packages.
What you can't have is multiple major versions of the same package in the runtime closure of your application. It's fine to have multiple versions of build and test tools, but you can't deploy multiple versions of the same package via a VFI, which includes just the runtime closure. (You also can't have multiple packages providing the same file at the same path, but it is surprising how uncommon that is when you think about it).