There is a Baal Shem Tov story (one version of it is here) where a couple who couldn't have children, had a child due to the Baal Shem Tov's blessing. When the child died on his second birthday, the Baal Shem Tov consoled the bereaved couple by explaining that their child was the reincarnated soul of a great convert who had to come back down in this world in order to rectify the first two years of his life, where he was "conceived, borne, and fed for two years in the spiritually negative environment of the royal palace."
Based on this story (and I'm sure if I looked I could find sources in Kabbalistic works dealing with reincarnation), we see that sometime a soul has to be reincarnated for a short period of time in order to rectify a certain blemish.
In this letter, quoted in this answer, the Lubavitcher Rebbe brings the opinion of the Arizal, that the heavenly voice calls out "This person is destined for so-and-so" only the first time the soul descends into the world. Not every time a soul is reincarnated the soul's intended match is reincarnated with him.
So, if we could make an assumption that when a soul is brought down to the world for a very short time it is in order for the soul to have some kind of rectification (that requires only a short time on this earth), it would make sense that the soul's intended match is not reincarnated together with him. (Even though the soul does have a match and the before the first time it entered the world the heavenly proclamation was made).