1) Having unchecked "Auto Select Next Unit", if a unit does not have move orders (is stationary and not set to guard or waiting to move somewhere), the unit will automatically be selected at the start of the next turn, yanking the camera away from wherever you had it and also deselecting whatever you previously had selected. ETA: This also happens to units without move orders who are already selected; the camera centers on them anyway. Level of annoyance: Extreme. (Having to move the camera back where I had it wastes my time.)
2) On the tactical map, if a unit's turn comes up and it is too near or outside the current camera frame, the camera centers on them. If the unit in question is a ranged attacker, this often winds up putting the unit's intended target out of the frame. Level of annoyance: Average. (It does not happen too often, and can be mitigated somewhat by zooming out. However, having to zoom out to mitigate this issue is, itself, annoying.)
3) On the tactical map, moving the camera with the arrow keys does not work. Level of annoyance: High. (The mouse has enough to do already, I shouldn't *have* to use it to scroll as well.)
4) The "Edge Scroll Speed" setting effects the rate of scroll by keyboard as well. A low edge scroll speed is needed in order to keep keyboard scroll speed from being insanely fast, but this, notably, makes edge scrolling very slow. Level of annoyance: Low. (I mostly rely on keyboard scroll.)
5) Keyboard scroll speed rate needs to be adjusted somewhat based on zoom level. When zoomed in fairly close, the rate is way too high, requiring a very light touch on the arrow keys to keep from moving too far at once. Level of annoyance: Average. (Easily adapted to, but realistically should be tweaked anyway.)
6) The "Edge Scroll Speed" option has tick marks in between the hundred-points, but can only be set to a number evenly divisible by 100. Level of annoyance: Trivial. (It's an aesthetic thing, just remove the bloody tick marks = P)