I'm annoyed at myself (and you're gonna hate me)... but I just played through this quest again. Right, ahem, Once you've dealt with the bandits and meet jack at GMS he says "I was just about to leave. I never thought you should (would?) make it", so he definitely was there before you dealt with the bandits (I really don't see how he'd slip past, 'specialy if you use grenades or AoE attacks. Plus I mince those guys, he woulda been behind me, or not very far in front, or caught in the crossfire). This is (to me) confirmed by what he says next "I knew I was being watched so I had to use a decoy to get the real package out of the station"
So he was being watched. I.E (how I'm reading this anyways) he was being followed/spied on WITHIN SGS, and maybe before he got there (anyone can get in it seems even if they're not a citizen, for trading etc), so you were being watched as he set you up as a decoy so you were the target now, and not him (allowing him to make an instant exit and be ignored by the conveniently placed thugs, or even managing to pass before they get there). They can't watch him from outside, someone was watching him from inside and see the deal you make , thus inform the thugs "new target, hes trying to do a fast one, someone else has the package" Oh, fast one indeed the sneak LOL. Then all eyes are on you, you're now being watched and jack is free to make an exit.
So I guess the package isn't necessary, just you being seen as the package holder is enough (plus they know you have a package, as epli said, using intel. But more specific than just 'hassle anyone who comes through')
In this case I wonder if the thugs should be more hidden, so all seems fine and then suddenly they come out of the shadows/from under the subways (or maybe walk up to you, as if they have just turned up). That'll make it seem more like an ambush and not like they were just hanging out there.
The spy intels them when you leave the station, by that time jacks long gone, but the thugs just standing in open makes me question how he'd get past (his stealth cant be that good at Lv15, it's not exactly an OP ability), and even though hes not the target any more, hired thugs would probs kill him anyways for a bit of profit (they seem more like hired muscle than spies) That package musta been damn important. Also, if I am right, maybe even have a shady or at least an extra person lingering in the cafe, maybe have him brush you away or ignore you if you try to initiate dialogue (whilst everyone else says something generic, making him seem suspect but not obvious, until jacks plan is revealed to you at GMS) or one of the weird spy bug thingys can scuttle about behind you/near you every new area you enter within SGS after you accept the quest (but obviously not able to destroy it, running in an out of ventilation shafts etc)...
Though, chances are maybe later encounters with JAck will shed more light on to this whole situation (who hired the thugs? whats in the package, was it stolen from someone and what is its importance etc)
Sorry peeps, that is all. you'll be happy to know I'm done picking this one apart and haven't currently encountered any other quests that make me question its nature.