A problem that can arise when not everyone can make it to the table is that someone running the absent person's character may make choices or decisions that are either out of character, don't sit well with the party, or don't sit well with the absent person once said player returns and exclaims:
"You did what? That isn't what my (character) would do!"
The original scenario is from Can divine smite be non lethal?:
... the player that plays this paladin missed the session, and the paladin's actions before have danced on that line between vengeful and mercy. The player replacing him only wanted to smite because his damage otherwise would reduce the enemy to 1 hp, and then rolled max damage for smite. I then gave him the option of not smiting and let it go another round or smite and kill. They left the decision up to the roll of the dice and ended up smiting.
While this was about the "kill or knockout" decision in combat, numerous in game choices confront any of us playing another's character for an evening. This has more to do with RP elements of playing a character, not any tactical error or omission. Since other players are at the table anyway, the tactical issues can usually be addressed in situ.
Our current group is faced a missing player frequently, as various work and family schedules mean that we rarely get all of us to the table at once. (Other than the GM, who is a gem!) While I have yet to encounter this sort of friction in our current group, I've seen it before and it can lead to interpersonal friction.
This inquiry is related to How do I deal with absent players missing out on levels or XP? and How do you plan a character's actions when the player is absent?, but narrows it down to "we decided to have X run the absent player" as the point of departure. I thus don't think it's a dupe.
What is the most effective way to resolve this conflict—either as players or GM—successfully so that it is acceptable to the party, is acceptable to the absent player, and prevents this becoming a problem in later sessions?
The answer "don't have that character played for that session" Is Not Acceptable.
In many cases, keeping the group together is needed for XP progression, party balance, and the continuing story line of the party remaining as cohesive as RL schedules allow.