I had a bunch of CLs with a dependency tree between them.

The "root" of the dependency tree https://chromium-review.googlesource.com/c/506307/ failed to pass the CQ because there was an infra failure (https://chromium-review.googlesource.com/c/506307/#message-bbe5e3090fec774424f95ce99143043af4743a05) and was retried automatically. So far so good.
However, all the dependent CLs (e.g. https://chrome-internal-review.googlesource.com/c/376330/#message-ac43f533e4d999fceb1735ae7632d3488741b611) were not automatically retried and even lost the CQ+1 because https://chromium-review.googlesource.com/c/506307/ had been "rejected" by the CQ.

Since https://chromium-review.googlesource.com/c/506307/ had not actually been rejected and was automatically retried, the dependent CLs would have ideally been retried too, and in any case shouldn't have lost the CQ+1, which needs to be manually reapplied.