In a CI job, using source control as the source and including deleted items, you can run into an issue where objects from managed packages show as "deleted" in terms of custom object permissions from permission sets that have access to them. This can occur for permission sets designed to give access to managed package features or if you have a permission set with "View all data" or a system permission that gives them access to all objects in some capacity (read, write).

Ideally, we wouldn't have to include managed package object permissions into Source Control (likewise, Gearset suggests only including installed package metadata versus the details of said package).

It'd be great if Gearset would exclude the custom object permissions being deleted if it's related to an object in a managed package

OR

Add a blocker/warning about trying to remove custom object read permission on a permission set that needs access to all objects (with "View all Data")