There were 42360 returnees (Ezra 2:64). Yirmiyahu 52:30 says 4600 people were exiled with Tzidkiyahu. Melachim 2 24:14 says 10000 were exiled with Yehoyachin. How can Temurah 15b say the majority of returnees were still alive in the days of Tzidkiyahu?
This is an interesting question. In truth you are writing about two of the various exiles, however ther were more than that. Sancherev alone took the Jews into exlile three times. The first time he took Gad, Reuvain and part of Menashe, see Melachim 2-15. The next time he took Zevulun and Naftali, later he took the rest of the ten tribes. What was left then was Yehuda, Binyamin and some of Levi, and it was from those that comprised the exlies of Tzidkiyahu and Yehoyachin. Therefore there were plenty of other people in exile to comprise the extra people.
See also Koheles Rabba 9, Abarbenel Hoshea 1-5