I also noticed this and was just playing around with it, I'm pretty sure it's a 3D problem.

If I rotate the camera so I'm looking straight down at the map, the click will focus right at the top of the cursor (at the tip of the feather).

If I rotate down as close to the horizon as possible, the click will land about half a tile above where it should.

[edit] This all happens with the hardware mouse too.

Interesting.  Definitely seems that the cursor needs to not be a 3D object, or at least not be floating off the ground, because no matter how well it's done, it's still going to lead to confusion from some angles.  I think the idea from another thread of having the square the cursor is on light up so you can see where it is, would be the best way to go.  Can't have misclicks in a turn-based game since that could spell the difference between heading off an attack against a city or not.

Well that would kinda help a little. But the better solution would be to make the square that you clicked on actually be the square you clicked on.

Yep ... me too ... I need to change camera angle to select the right spot.

I agree it is easy to click in the wrong place by mistake, they do need to improve this at some point before the release.

I've also had this issue, seems to work better in windowed mode, possibly "stretching" the content across my screen adds/creates the problem.

I can also reproduce this problem. I wonder if it's related to using a widescreen resolution? I"m running the game in 1280x912 on a widescreen monitor.

DXDIAG: http://pastebin.com/m30680174