I agree with Ari in the idea of introducing them trying to learn each other's language - starting out with simple things like "Stick"/"Qarti", "Rock"/"Bqtal", etc., but don't belabor the point. It might be a good chapter/scene break going from introducing language difficulties, to speaking broken language, to one or the other getting fluent in it.
Even if you had a "universal translator", it would still need time to gather words/phrases/sentence structure before it could turn out a decent translation, either direction. And, don't forget, even if Person A or Person B learns the other language, they might slip back into their own language in a high stress situation, leaving the other person confused (and possibly in danger, if the first one is telling him to duck and he does it in the wrong language).
If you can find it, the movie "Enemy Mine" had a good section about two opponents who're forced to work together to survive crashing on a planet.