a very large community with millions of subreddits. The data is very fluid meaning that subreddits are constantly changing their privacy settings, etc. Generally what happens when a comment or submission is found that wasn't in the original dump is that the object was ...
Conversation
...originally part of a subreddit that was private that then later went public. When a subreddit goes private, the Pushshift ingest no longer sees any activity for that subreddit. This generally only affects less than .01% of all available objects from Reddit's API.