EDIT: it DOES happen in Alpha, too. Perhaps less often.
I want to say this was really, really disconcerting and hard to pin down and I think you should release the Alpha release ASAP because this drove me insane.
Right-click choose menu (like empty trash) and about 50% of the time it would miss the click and I'd have to redo it. Honestly, I thought I was going crazy until I quit BTT and it completely stopped happening.
And it happened on 2 machines (work, home).
I can make a video of it happening, if that would help.
could be some other app conflicting with BTT, any other mouse or keyboard related apps installed?
Yes, I have other ones installed, but I just went back to version
https://folivora.ai/releases/btt3.786-1931.zip
and it doesn't happen on this one.
I have AltTab and SaneSideButtons installed, but I quit those and still saw the problem with BTT.
I will report back after using the older version for a while, but so far it's working fine.
No problems since I started using the older version mentioned above.
Not sure what else I can do to help find this. No one else is seeing this?
Btw, I'm on macOS 12.5.1 on an M1. Both home and work.
https://folivora.ai/releases/btt3.821-1964.zip does not exhibit the problem. Turns out I was on this at home. I've updated to the latest (non-Alpha) at home and will report back.
If it doesn't happen on the home machine, what do you suggest to diagnose the issue on the work computer?
Didn't have the problem at home. Work hardware is iMac (24", M1, 2021). 12.5.1, as I said (both home and work).
The older version does NOT have the problem, the newer versions do.
Ideas?
No ideas right now (no other reports so far and doesn't seem to happen here), but I'll keep monitoring this. Maybe it's already fixed in my current development build.
I had same problem as OP. Really annoying problem of making sure your mouse click goes through and often have to re-click slower to make it work.
I downgraded to 3.821-1964 and the problem is gone.
macOS Monterey - Version 12.5.1 (21G83)
iMac (Retina 5K, 27-inch, Late 2015)
EDIT: Come to think of it, in my very amateur testing and troubleshooting, it felt like the mouse was double-clicking with a single click... and/or also it felt as if this behaviour happened when trying to click while the mouse was slightly still moving. I don't know... maybe I'm just high.
Possibly try the latest alpha versions (>= 3.842), I haven't experienced any mouse issues with these builds, so maybe this is already fixed
Testing 3.843 (1990)
Will report back.
Everything OK in versions 3.843 & 3.870 
Using 3.870 on the machine I originally had the problem. So far, my quick tests have shown no issues. Will report back in a few days.
Pretty much a whole day without a problem, so I think the latest version fixes it for me, too.