what can you as an individual do to prevent this from happening?
As an individual, not a whole heck of a lot. Mistakes with lethal consequences do happen as a matter of chance, whether from confused law enforcement officers or from a slip with a power tool, or an inattentive driver. Most of the things that endanger our lives are orders of magnitude more common than these kinds of mistaken entries.
What can you do to reduce your chances of this specific problem?
Don't do "stupid" things with "stupid" people which helps you avoid tangential associations that could bring you this kind of attention.
Make your home reasonably "hardened" and alarmed so that you aren't caught completely unaware by intruders -- whomever they turn out to be. (Get a dog -- even if they are quickly neutralized, they will make noise and alert you before the first thump on the door.)
Work out good lighting for your home that can be activated remotely, so that once you know someone's attempting entry you can see who it appears to be.
Have a plan to respond in an effective way to any unexpected entry. This shouldn't probably be kicking open the bedroom door and opening fire with a shotgun. More along the lines of hunkering down behind cover, making intruders come to you through a choke point you control, having someone contacting 911 as fast as possible.
None of this might have saved this man's life, but the shoot/no-shoot decision is made extremely quickly. Explosive confrontation is generally the worst way to proceed. (Even if you take down the first intruder you see, you aren't going to prevail against a whole SWAT team and once the shooting starts it probably won't stop until you're no longer in a position to care). A single second more for all parties to evaluate their next move might have made the difference. The earlier in the event you are awake and thinking the more chance you have of making yourself known as an innocent, and making wise choices about how/when to show yourself and/or who to shoot or not shoot.