I do not have a confident recipe for this, but I've observed it multiple times today, and just realized what's going on.
I have several Orion windows open. (Across two monitors, although I suspect that's not relevant; all of this is happening on one of these monitors. All of the windows are full-screen; I use Mac's three-finger-swipe gesture to switch between windows more or less constantly.) Each window has a large number of tabs open, and I switch between windows frequently. (The windows are basically task-centric: one for work, one for blogs, one for general personal, etc.)
Gmail is pinned, which may or may not be relevant. (Side note: I really, desperately would like that pin to only be in a single window, the way it works in Chrome. In practice, my pins get copied across all of my windows, at least after some restarts. This is livable, but constantly inconvenient and confusing -- I expect pins to have a window affinity, same as ordinary tabs.) In practice, I use the pinned Gmail tab from the Personal window, but am spending most of my time in the Work window.
Multiple times today, I've been reading an email in Gmail, and been mystified that absolutely nothing visible has happened. This left me thinking that Orion was somehow broken.
Only after restarting Orion did I realize what had occurred: the links did open -- but in the wrong window. And as a result, focus didn't switch to the newly-opened tab, so I thought nothing had happened. (Post-restart, I discovered a big pile of tabs that had opened in the middle of my Work window's tabs.)
So the issue presumably has something to do with focus -- in between working mainly in the Work window, but periodically swiping over to the Personal window to read Gmail and click on links, Orion appears to still think that the Work window is focused, and is opening tabs there instead of in the same Personal window where I'm clicking on the links.
As mentioned above, I don't yet have a clear reproducer (and I'm about to be busy for several days, so probably won't have time to investigate further), but thought I should bring it to your attention. I suspect this behavior is new -- I haven't noticed it before today -- but I'm not sure.
Links that open a new tab should always do so in the same window that was clicked in.
Version 0.99.130.2-beta (WebKit 621.1.2.111.4)
Sequoia (15)