When this happens to me, the problem is that I'm not steady enough in my line selection. So I'll briefly be selecting two lines of input. And when the other line of input is shorter or even empty, it resets to the rightmost edge of that line (which if empty is the far left). Being very careful when moving horizontally can work but is difficult to maintain. Perhaps turning down the mouse sensitivity would help.
Searching for "eclipse line wrap" found that Alt Shift Y turns line wrap on and off. There also seems to be a button on the toolbar. See Does Eclipse have line-wrap for more details.
As others have noted, changing so that the lines aren't wider than the window also fixes this. But when you're in a situation where someone else sets the line length, toggling line wrap can be a quick and easy solution to this problem.
This of course assumes that you are having the same problem as me and not something caused by a plugin or other issue.