Hmm, selecting planets sounds like a better workaround than what I've been doing. I found that the way to avoid it was to click on the square with possible problems, and make sure that every ship or fleet there is deselected before moving on to the next ship. The problem seems to happen when you have multiple ships/fleets selected, then move to annother ship. It doesn't tend to deselect the ships properly (sometimes the first one is deselected, sometimes they all stay selected) and clicking on annother ship only adds that ship to the selected group, it doesn't clear the first group.