As a general advice to Judges at a tournament, don't expect every single infraction to be spelled out exactly in the penalty guidelines. They are only guidelines, not a comprehensive and inclusive book of rules.
Obviously, in this case, something that was done was not correct. Players can't just reach over and shuffle their opponent's deck at any time that they wish.
But the specific case is not spelled out exactly in the rule book.
The procedure to follow is to first determine what class of ruling it is.
In this case, a Game Play Error.
Second, the judge should them look at the definitions given for the different levels (Minor, Major, & Severe) and see which one fits the infraction best. If still unsure, the examples given should be used as a guide to help place it into one of the categories.
If one of the examples given is an exact match, that is a BONUS, not a requirement!
Then, the judge would look at the recommended penalties, taking the level of the tournament into account. An LC would be a lower level event, not held to the same standard as a Regionals or Nationals.
Finally, the judge should determine if there are factors that should adjust the penalty up or down, such as age/inexperience of the player or if there have been repeated infractions already.
A judge should never, ever expect that the exact situation they are experiencing is explicitly called out in the guidelines.