I believe this to be a bug, but it might be intentional. In any case, the current functionality is, in my opinion, poorly conceived.

If a user adds a deletion to a comparison between an org and git, the deleted metadata is the only item that will show up in Gearset. However, if you inspect the resulting commit in git, you will see that the metadata was deleted along with all of the profiles, layouts, etc that had to be changed as a side effect.

I'm completely fine with Gearset detecting these dependencies and making the changes to them. It makes sense!

I'm NOT fine with Gearset never actually showing me the list of changed items due to these side effects.

Thus, my suggestion is for Gearset to always include the full list of changed metadata that will be pushed to the target org/source control. Even if that type of metadata is not a part of the original filter.

For reference, here is an example that a Gearset employee was able to produce.

Apex class deletion in Gearset:
https://gearset-b442bc7f2cf1.intercom-mail.com/i/o/141563438/5255f13a74f6114073275083/File1565950331859

And the resulting commit over in github:
https://gearset-b442bc7f2cf1.intercom-mail.com/i/o/141564016/2f209aca43e7a48b6d492285/File1565950510246

I believe that Gearset should show the same list of changed files that end up being pushed into Github.