The community bot has 5 reputation: why is this? Also, its Main User has 1 reputation, and only the Meta user has 5 reputation, which doesn't usually happen; even with people. Is this a bug?
The Community user is special, as is explained on Meta.SE.
It's a bot operating on the entire network and it's reputation doesn't mean anything. For example: if you flag a question as spam the question is automatically downvoted as well. Somebody has to be responsible for that downvote, so it's attributed to Community. It doesn't have the reputation to do so, but that doesn't matter. It's a very special bot.
Community is active on every site. Community changed all Stack Exchange links from
https inside posts when the support for it came on-line. It can reject edits, turn posts into a community wiki and a lot more.
Well, automated scripts do. And whenever actions need to be attributed to someone and it's done by an automatic script, it's attributed to Community.
Long story short: Community's reputation is irrelevant and it's not a bug. Simply a special case.
Have you noticed Community's user id?