I suspect you used your multi tool incorrectly. If you plunge the tool to full depth then cut forwards etc it will wander all over the place
Instead place a straight edge on the floor, use the cutting head that looks like pacman, turn on the saw and run it smoothly, and consistently back and forth along the straight edge, gradually cutting through the floorboard in increasing depth. The end result of the cut should be a much straighter line than you would achieve otherwise (freehand etc)
If the pacman head doesn't cut deep enough you can switch to a straight / rectangular plunge cutter after Pac-Man reaches max depth, because the sides of the cut will then define the straight edge for the straight blade to follow. Set the blade at 45 degrees on the machine and then when running the cut have it at maybe 10 or 20 degrees off vertical and cut in the same way (gradually increasing depth) rather than plunging and pushing forward.