This was a fluke. But flukes happen.
First: there are ways to mitigate criticals. One of the available core archetype abilities is "tough as nails", which lets a PC spend a story point once a session to turn any critical roll into an 01. There's also a "durable" talent (tier 1) which reduces crit severity by 10 per rank, and a "heroic will" talent (tier 3) which lets a character spend a story point to ignore critical injury effects for two characteristics until the end of combat. Enough to shrug off a little bad luck, certainly, but the thing about bad luck is there's no reason for it to stop happening.
Second: Two triumphs on the 2 Proficiency dice you rolled and three net successes for damage on the Ability dice, even after factoring in the difficulty dice? Every ranged combat action has at least 1 difficulty, and if you're running a combat against a group of minions, most minions just have a 2 characteristic so even if there's 4 of them you're limited in your proficiency dice by the lesser of characteristic and number. Also I'm assuming a 6 damage pistol.
I'm not saying it couldn't happen, but these were some ridiculous odds, along with the 80+ on the crit injury roll before the +10 bonus for a second one on the same attack. But the odds that it happened to you were 1 out of 1.
This is the case with all balanced-by-low-percentage game mechanics: they favor the side that's otherwise at a disadvantage, because "getting lucky" is a much bigger multiplier for them. I mean, the PCs were probably going to go on to another half-dozen encounters, while this group of thugs was ready to die here. But now they've effectively knocked out the PC's heavy and derailed the adventure.
There are a couple options for you as the game master, though.
First is to redirect the crit. There are other things to spend triumphs on than dealing critical injuries - for example, there's "accomplish something vital" or "disable a piece of gear". So instead of having to deal with three dice of brink critical on their heavy, now the PCs have to pull off the heist with some vital piece of kit broken and the alarm going off, which are things they have skills to mitigate as a group instead of needing godlike doctor skill on any one PC. You can just decide not to spend minion triumphs on going directly for the jugular (though their damage can still stack up to do it normally) and save that for the big confrontation with rivals or nemeses.
Second is to not pull your punches, and tell the players so. Any fight to the death could potentially turn ugly. If you want to run a less shoot-em-up game where you expect players to sneak around, fast talk, and misdirect, and only get into combat as a last resort, you can always go full deadly, whatever the odds.