1- Truce among Rogues: I noticed that, once upgraded, this ability not only makes the neutral forces guarding each planet allied to you, but also makes the pirates allied to you, which is what the later diplomatic upgrade is supposed to do, I believe?

Once you get Truce among Rogues, bounty becomes irrelevant as pirates will never attack you.

2- Speaking of pirates, the Bounty indicator, at the top right of the screen, below the black market resource display, does not function properly. When you have the highest bounty on your head, it does not display your name so you can't really tell you're the one with the bounty unless you see the little message saying "Bounty against your empire has increased".

I've seen a few more but they've been noted in the Known Issues thread, such as Titans blocking movement for other ships, preventing them from getting into a group phase jump formation, neutral planets cannot be colonized after researching Truce among Rogues, Titans going after strike craft.

Aside from these bugs, I'm enjoying Rebellion greatly, can't wait to get to play the Advent either.

Personally though, I find that the Titan upgrades are very early in the tech tree, although I would assume you've made it easier to get in the Beta because you do want people to get the Titans and fly them around and plan to move them further into the tech tree later on?