An examination of the details shows that there were Israelis who received a permit, but did not manage to reach the country of origin (USA, Dubai, etc.) to Germany, from where the rescue flight departed.

The first rescue flight took off this morning, around 10:00 and will land at Ben Gurion Airport shortly before Shabbat. The next rescue flight will take off on Sunday to Frankfurt, and is scheduled to take out passengers from Israel who will receive a special permit, and return Israelis with similar permits.
If Ben-Gurion Airport remains closed beyond Sunday, the expectation is that the state’s agreement with Israir will continue, and more rescue flights will depart. The airport will currently remain closed until Sunday night, but the prime minister and health ministry officials have already announced that they will most likely request an extension.
Yossi Weizmann, an Israeli who is currently on the flight, told Israel Today: “Due to medical reasons, we had to return to Israel as soon as possible. “This flight did not work out. Miraculously, my agent managed to find us a ticket from Dubai to Frankfurt and from Frankfurt to Tel Aviv.”
The rescue flight that will take off for Israel on Sunday will have 16 Israeli passengers who flew to the celebration in Morocco and got stuck there. Passengers will travel a long and difficult way to get to Frankfurt and from there return to their homes in Israel.