The former Juventus midfielder was brought on for the last half hour with the score at 0-0, but failed to make an impact and made several errors – including a woeful misplaced pass that went straight out of play – leading United great Roy Keane to describe his performance as "schoolboy".
Conversely, Kondogbia has enjoyed a terrific loan spell for Valencia since joining from Inter and was influential in the 2-0 win against Sevilla last weekend that left them 11 points clear of their rivals in the battle for fourth in LaLiga.
However, Kondogbia was not included in France's squad alongside Pogba for upcoming friendlies against Colombia and Russia and won the last of his five caps in September 2015, something Marcelino is perplexed by.
"Kondogbia didn't only play brilliantly against Sevilla, but he has had a lot of excellent games throughout the entire season," he said ahead of Saturday's contest with Deportivo Alaves.
"He is a key player for us, he is important for how we play and although I don't follow how the other French midfielders are getting on, recently I don't think that some of them would be close to how Kondogbia is playing.
"We saw Pogba play against Sevilla and Kondogbia against the same opponent and there isn't any kind of comparison to be made.
"As always, however, I have total respect for the national team managers and as Valencia boss I am happy that he is here with us."