In the video, the enemy capital ship gets disabled after the 3rd shot or so, so there are 7 remaining shots that just uselessly hit the disabled ship. Immediately after disabling, the charges on the burst cannons get set to zero, but by the end of the volley they somehow start charging again. Switching to fewer bullets on the 2nd node makes it no longer happen at this particular HP value, but going down another 100 distance (so you start 1/2 shotting instead of 3 shotting) makes it happen again.
This is one of the main reasons why burst cannon is so much stronger than capital laser for farming at overpowered stats.