Profiles are different to many other metadata types on the metadata API. The subcomponents returned by Salesforce for a profile depend on the other metadata types in your metadata filter. More information on Profiles can be found here.

For example, if you select just the Profile metadata type in your custom metadata filter and run a comparison, you'll get only the user permissions of the Profile.

So which metadata types should you include in the custom filter to retrieve each individual part?

We created a Default profiles and permission sets comparison filter for those of you that don't need the details further below. Not sure how to manage your custom metadata filter? See here.

Here is a handy reference table showing you which other metadata types you'll need to include in your filter to get each subcomponent type in your profile:

Since this is under component in the table, select the profile with the FLS changes and using the dropdown arrow, find components.

In my metadata filter I have Profile and Custom object selected. Once you have expanded components you should be able to see all the FLS that you expected to see.

Since this is under Top level in the table, you can see the Apex class permissions in the comparison table.

In my metadata filter I have Profile and Apex class selected.

Gearset also makes it possible and easy to deploy the permissions of an item across multiple profiles and/or permission sets. The following 6 groupings of metadata types allow you to deploy the permission of not just one profile at a time, but of multiple profiles in one go.