Tweets in my Tweetbot timeline are occasionally marked as a favorite when I see them for the first time. Is that a bug or a feature?
It's a bug with Twitter, not Tweetbot.
I've seen people ask @tweetbot about it several times now. The answer and response generally look like this exchange:

Q: @tweetbot keeps favoriting random tweets in my timeline. It's almost embarrassing.
A: Sorry, that's a Twitter bug. As you can see on Favstar, they're not real favorites.

That particular exchange happened just yesterday.
Twitter's REST API bug list has this bug still open where the API may erroneously report a tweet as favorited when in fact it is not.