In most RPGs, if the party splits up, it's a detriment to the PCs. Resources are spread thin, they can be overwhelmed and ganged up on, etc. What's more, several players sit around twiddling their thumbs while 20 minutes (or more) of combat drag by. But that's just not the case in 3:16 Carnage Amongst The Stars. It's not like D&D where 6 ogres is a much biggger challenge for one player than for the whole party assembled. The fights are fast and really abstract, and if the isolated troopers have a Strength to spend, they can take out as large a pile of Threat Tokens as the GM deems to put before them. Splitting up, going out alone, etc, is all a huge benefit to the PCs that engage in such antics - as they'll get the most kills and rarely get punished for it.
As GM, you want to reward such behavior when the PC takes some big risk (night watch, recon patrol, searching a tunnel complex, or other situations of significant peril or isolation) or is enhancing the game in a meaningful way (figuring out a complicated situation, developing character by storming or goofing off, cleverly setting up a trap, etc), but not for just every-day "I go through the door first" antics.
Or so I think.
But I could see the other side of the argument. It's a competitive game, and thus anyone whose willing to take a risk (no matter how small) should be rewarded. I'd be in that other camp, if the scope and scale of the system were a little less expansive. "I'm first through the door of the hut, so I get to kill d100 baddies before anyone else follows me" is a bit extreme.
It would be really nice if the GM's section of 3:16 had covered in any way the notion of splitting the party. It seems to assume this will never come up, which strikes me as a little odd, given that it's relatively easy via the advancement system for a party of 4 PCs to be a Trooper, a Sergeant, a Lieutenant and a Captain. Four characters of such a diverse spread of ranks shouldn't necessarily always be at the same post. Late in the campaign, when all the PCs are likely to be Officers leading their own units, it becomes even harder to justify all the PCs being at the same battle. Not a major flaw, but more than a tiny bit annoying.