Thanks Adrian, that is interesting and yes the documentation says that the yellow pencil indicates a custom application, but these are definitely not ones we have created. However, they do have the option to disable app-id so that fits in with them being customisable, rather than custom applications.
We noticed these after we upgraded to v10 and as far as I can tell the red cog is shown on all applications in a group, but we have not changed anything on them. From what I can see they don't have anything that can be modified.
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