You have to be a certain distance and at a certain angle as well as have a fase line pointing behind you. Its tricky. I just tried to reproduce it again and it took my 20 min to get it right and I knew what to try for. It happens often enough that next time I will get a screen of it.

I was finally able to reliably reproduce this. I am 95% sure I know what is happening.

When you are looking down on an object, there is nothting between you and it, generally speaking. If there is, whatever is "farthest" from the "table" will be selected when you click. What is happening in this case is that when you bring the "camera" down to a low level, your view is sandwiched between somewhere you are trying to click on and an object, in this case a planet, which is behind your point of view. However, your point of view is not the limit of the input. The "imput" is actually behind the camera, and behind the planet, so on this new plane the planet is now "above" the table and below the imput and gets selected. Remember, the table is only selected if nothing else falls under the cursor.

That explination, kind of sucks, let me see if I can illustrate.
T=Table, C=camera, I=input, P=planet

T C I P
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If you think of it as layers in the direction of the arrow, the table is the bottom plane, the camera is "above" it next, the input( where the mouse thinks it is) is right behind the camera and the planet is beind the input. When you click, it searches from right to left to find a valid item to select. If nothing is detected it defaults to the table or surface. So when you try to move, you end up were you want to be. The camera is "invisible" or "unselectable" so doesnt count.


T CPI
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In the example above through dumb luck the planet ended up behind the camera, you can't see it and do not realize it is there. However it is below the top layer or imput and is a valid selection (unlike the camera itself) and so the planet is selected. So wheather you right-click move or use the move command, you are really selecting the planet and thats where your fleet will move.

Hope this explination helps people understand and avoid the problem... basically, look "down" if you can if you cant, zoom in so that where you want to click is just below the camera.

I could be wrong, but my tests show I am at least close to the root of the problem. Should help in reproduction.

I have had this bug as well, but since I don't angle my cam that much in game (no real strategic/tactical value to do so) I was looking straight down on the grav well, I was zoomed out as far as you can be and still see the grav well. I clicked on a point in the grav well to tell my ships to move and instead they chose a random phaseline to jump through. The phaseline does not have to be heading straight behind you, I have had the ships choose a phaseline to the upper right, upper left, straight up, and any number of other directions from the camera's point of view. My work around for this problem is that I have just simply stopped playing at that zoom level since it is ineffective. But it would be nice if I could give general movement orders from that zoom level, since it allows me to keep an eye on other planets in the area while i'm still microing an engagement or prepping a fleet to receive enemies.

EDIT: Ok, I just reproduced the bug reliably, and it doesn't happen when I am in a purely straight down view, but it does happen if I tilt the camera a couple of degrees (less than 10 degrees?). I'm not sure exactly how many degrees tilt my camera has when it happens, but it isn't an "extreme angle" by any means