1) Effects UI - this is a real flaky one. Say you have your shape selected in paint/animatte, or say you have your layer selected in 3dwarp, it gives you a white outline in the UI right? You can click on it, move it, resize it etc... it usually works as expected. But often I've found that the UI feedback completley breaks down. It'll show that objects are selected when they're not, and vice versa. It's a complete mess when you're dealing with multiple objects on screen. The culprit? I think it's that daft little Color Info palette. Every time I get an eyedropper out it pops up and things start to go awry. If I close it down, the UI seems to go back to normal.
2) Zooming in the record monitor - I have zooming in/out mapped to my keyboard so I can zoom into the picture when I'm either in S/R mode or effects mode. In recent versions I've noticed that when I'm zoomed in by a factor of 1x or more in S/R, and I switch to effects mode, the zooming functionality breaks down. Either the image is pushed into the corner, dissapears or I can't get back to full image. I have to go back into S/R to zoom out in order for effects mode to work.
3) Another zooming one - I think this is a new one with 8.6. When zoomed in S/R mode, if you hit CTRL ALT to get the hand grabber and move the image all the way to the LHS, as soon as gets to the edge the image pops back into central position. Weird.
4) Audio plugins - if you try and open a audio plugin in 8.6, either through the AudioSuite window or as a track effect, the UI won't show. Why? It's hidden, and you need to hit Windows>Center Current to make it show. But this doen't always work, particularly with track effects.... the only thing I can do is restart. Annoying.
5) Tracking - this one's existed for ages. It's an issue (I think) with switching between interlaced and progressive. Say, you track in interlaced and then switch to progressive, you'll often find that your tracking object drifts to the top left towards the end of the effect. It's the SteadyGlide that's responsible - disable it and problem solved, but if you need SteadyGlide enabled the only thing you can do is re-track. For me, it's a common problem with stabiliser - SteadyGilde is on by default. I've lost count of the number of times I've had to say 'Oh it's an Avid bug' to clients when we're watching back a finished program and all of a sudden the stabilised image drifts up to the corner of the screen.
There is more, I'm sure of it, but I can't think back just now. I'll add to this list when I get a chance. It would be excellent to see these issues resolved in future releases!
Sion