This was addressed in the first episode of Season 2. Winn decrypts Mon-El's flight-recorder and they find that he was trapped in a region of space (known as the ["Well of Stars"][1]) where time doesn't flow normally.

> **Winn:** *Now, it seems sleeping beauty on his journey from Krypton passed through something called the ...* [pauses slightly] *"Segara
> Beyal"* 
> 
> **Kara:** *The Well of Stars. My father took me there once. Time doesn't pass there. So that's why he's still so young.*
>
> <Sub><sup>[Supergirl: The Adventure of Supergirl - Transcript][2]</Sub></sup>

[![enter image description here][3]][3]


  [1]: http://arrow.wikia.com/wiki/Well_of_Stars
  [2]: http://transcripts.foreverdreaming.org/viewtopic.php?f=297&t=28987
  [3]: https://i.sstatic.net/YGtrg.png