Karl Mordo was a huge role in Doctor Strange and there's no explanation for where he was in Avengers: Infinity War. If Wong was there Karl should have been too.
If Wong was there Karl should have been too.
Just because Wong was at the New York Sanctum with Strange doesn't mean Karl would be.
At the end of Doctor Strange, Karl felt disillusioned due to repeated breaking of the laws of nature after learning about how the Ancient One was siphoning power from the Dark Dimension and how Strange manipulated Time to defeat Dormammu, because of this he left the Masters of the Mystic Arts and doesn't want anything to do with them.
now if you ignore his name being that of a super villain in the comics, Baron Karl Amadeus Mordo, the only indication that he has a future appearance is the post-credits scene of the movie where it's suggested he's now hunting Sorcerers
Mordo made it clear he had left the Masters of the Mystic Arts and, when Pangborn realized that Mordo was going to attack him, he then retaliated with a crowbar. Mordo defeated him and began stealing his magic by drawing it out of his chest, reducing him to a paralytic once more. The horrified Pangborn clutched his own now useless legs and questioned why Mordo was doing this, to which Mordo declared his intention to cleanse the entire world of rogue sorcerers.
so not only is he not with Wong and Strange, it's hinted he will one day oppose them (possibly in the second Doctor Strange Movie) so he certainly wouldn't be fighting on their side.
At this point we can only assume that at the time of the Infinity War, Karl was hunting down other Sorcerers and may or may not have been part of the 50% that was wiped out in the end
Out of Universe:
This explanation would be that Marvel Cinematic Universe wanted to save Mordo until he could be the star of the show (so this would point towards him being the main villain in Doctor Strange 2).
The third -- and most likely -- choice is that we will really get to see Mordo start his arc as a villain in the not-yet-announced Doctor Strange 2. The benefit of saving Mordo for a direct sequel to Strange's first solo adventure would be that the narrative could really focus on the relationship between the former friends, and create deeply personal conflict without the distractions that come packaged with Marvel's capstone blockbusters. Sadly, this would mean not seeing the subject matter teased in Doctor Strange's post-credits scene until at least 2020 -- but we're willing to wait so long as it's quality.
This also makes sense because it allows Thanos to take up as much of Infinity War as possible.
The first option is that, like Strange and Wong, Mordo will make his next Marvel Cinematic Universe appearance in aforementioned The Avengers: Infinity War. The Russos and screenwriters Christopher Markus and Stephen McFeely have discussed at length their efforts to have the blockbuster include every available character we've seen in the franchise thus far -- and that's a list that should include Mordo. That being said, considering Thanos should be taking up most of the film's villain time, it probably wouldn't give him ample opportunity to really start executing his master plan.
There has been no in-universe explanation that I can find.
Edit: while all of the above still stands I have stumbled across one in-universe explanation. Mordo was searching for allies while the events in Infinity War were happening. It is very probable that Mordo will be going after Doctor Strange at some point, but he needs allies.
Of course, in order to take out Doctor Strange and all of the other masters of magic in the world, Mordo is going to need both a plan and probably some assistance. It's entirely possible that he himself could wind up teaming with Dormammu -- as one of the first major Doctor Strange arcs in the comics saw Mordo using power from the Dark Dimension to take out the Sorcerer Supreme -- but we'd be just as happy seeing him work with another new character. Perhaps it could ultimately be the Marvel Cinematic Universe's way of introducing us to Mephisto.
(Highlighting is mine) So, I believe that the most logical in-universe explanation is that Mordo was gathering resources and allies to take down Doctor Strange while the events of Infinity War were happening.