I scored ISU, DCRA and BCRA targets and other modern rifle targets for many years.
Those targets certainly look like only 2 holes to me, due to the permanent holes in the backing appearing as a single hole. What do those holes measure? When gauging holes for more than 1 bullet, a plug is normally used, unless using a moving backer. If the bullet diameter plug 'sticks' in the hole by the weight of the plug, then is judged as a single bullet hole. If the gauge falls through the hole, it is gauged as more than 1 projectile has passed. Sometimes the difference cannot be seen by the naked eye, but usually can, especially if more than 2 have been fired through it. Low velocity projectiles make reading single sheet paper targets difficult, especially if poor grade paper is used. With most ML rifles, a bristle board targets shows holes well- at least at close range. Target paper is especially formulated with short fibers, so the holes are not torn badly. The longer the fibers, the worse the tears.
As a single projectile cuts a slightly smaller than bullet sized hole in the material, I assume a ball certainly would, as well. If a bore sized ball stayed on top of the hole in the backing, I'd definitely say only one projectile passed through that hole, although the ball itself would have been slightly larger than bore size - but how much more?