Forgive me if I'm a bit blunt. This general subject has already come up, so it's getting pretty rote for me.
To reiterate for newcomers: Not catching a pokemon means we fail the test. Not catching the pokemon we said we were going to catch means we fail the test. Catching a pokemon in addition to the pokemon we said we were going to catch (and being found out) means we fail the test. Not being back at the drop-off point within two weeks means we fail the test. Failing the test means our character either gets shunted to the normal military or becomes a civilian, and we take control of another character. The same is true if we die, which is a very likely possibility. The QM would be perfectly happy to hand these consequences down to us.
If you're really interested in what could happen if we decide to try going for a second pokemon with the extra pokeball:
Only a rare and valuable pokemon would be worth the risk of getting caught. While we have no time now, we could potentially research one after our interviews. We have the time to fit one in along with the Kangaskhan research, iirc, given our access to Gary's files. However, we know from the distances and travel times we were given that it's going to be challenging to go deep into the Safari Zone, survive long enough to catch three pokemon, and get out in the span of two weeks. That one of those pokemon is very rare and dangerous will make it outright harrowing. It isn't just unlikely for us to go catch a second rare and most likely dangerous pokemon on top of all that. It's a pipe dream.
Even if we had more time, or were alone and didn't have to worry about anyone else passing, it would be pretty pointless. Only ultra balls or better hold pokemon in stasis. Given how tightly controlled regular pokeballs seem to be, we aren't going to get our hands on an ultra ball. We'd have to come back within a few days (with no access to flight options) or else the pokemon will just die of dehydration. That's all without getting into how difficult it would be to explain how and where we got it when we go to register it.
Overall, if we really have our heart set on a Scyther or Dratini or similar, we're better off just going back to the Safari Zone later.