Yep, file the joint as follows: _\ (exagerrated), instead of _| , the leading edge should then butt up close.
Laser cutters can't cut a perpendicular angle, especially in wood that thick. The point where the laser enters first will be eaten away more than the place it exits, leaving what would be draft angle on a plastic part. So you're starting out with
_/. File or sand it to
_| and you'll be all set.
I've heard the advice to file it to
_\ before... but the problem with that is when you go to glue it together you get a weaker joint that has to be filled with glue... or a strong joint and a pair of non-perpendicular walls. Then you run into trouble when putting the box together.
It's pretty easy to use the blackened edge left by the laser cutter to monitor your filing progress. Once it's all cleaned off, you know you've done the whole length of the edge.