Hi there! Thank you very much for your report - I have confirmed this bug with the following method:
1) Give yourself a pokemon with a multi-hit attack. I used a level 17 Litten with Fury Swipes.
2) Create a Trainer NPC with a pokemon that uses Substitute. I gave the NPC a Level 30 Rattata with only Substitute and no other moves.
3) The Rattata was faster than my Litten, so it used Substitute first, and then my Litten used Fury Swipes, hitting the Sub 4 times, killing the Sub, then hitting the Sub once more.
This issue has been forwarded to the Internal tracker!