The following is the reason for URL's showing only in the index
1. Google knows of the page because it has found a link leading to the page but currently does not have it in its index. That is discovery. It records the URL as To be Indexed later by another bot. This is typical with new sites and sites in which the page has been removed from the index for various reasons.
If your site or a particular document had been removed from the index for any number of reasons, some intention and some not intentional, OR your site is new then you will see the URL only in the SERP's until it is indexed. There is no partially indexed. Its either indexed or not.
DMC
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