I’ve seen the incident referred to in the OP. The matter of a PT would certainly come up in the after match debrief.
In terms of the incident in isolation I could support the referee not going for the penalty try because the first scrum went sideways, (YC - L/H) the second went sideways slightly and more or less up on the spot with an AR call that indicated the new L/H (the original T/H) may have been at fault, and lastly the third one saw the scrum nudge forward and the T/H slip to ground. (YC) The scrum was more or less in in the same position as it started; at best half a metre nearer the line. The ground was quite soft and not secure underfoot during the match so it could be said that perhaps the second YC was a big harsh. It certainly looked accidental. There was no clear opportunity to score a try by going forward in any of the scrums. Hence some sympathy towards not going for a PT. The second YC unfortunately resulted in uncontested scrums. If another scrum had also gone to a penalty offence then I would have expected a PT regardless of whether there had been forward movement.
However, these incidents should not be seen in isolation. Prior to this incident (only about a minute before) there were a series of scrums in a very similar situation with the same side which was under pressure giving away three similar penalties. This could have been taken into account because they had had a warning at this set of scrums as well. So there could be deemed prior negativity by the side in question. For this reason I would have supported the referee going for a PT on the second occasion.
Not an easy decision for the referee, especially if you take into account the score at the time. A PT would have given the lead to the attacking side with very little time left. Was the referee going to let the players decide the game rather like Mr Barnes did in the France/Wales game a few years ago? I would have liked to have discussed the game with the referee but I have no doubt that he will be discussing/reflecting on this game and the particular incidents in question in some detail in his review.