Coulson (and/or Skye) said there were four (or five) bases still with SHIELD while they were at the Hub. If whoever's left scrambling to claim items for SHIELD's side (not to mention Talbot's forces) see a bunch of convicts escaping from the Fridge, they'd presumably have weapons and vehicles against those on foot.... it just seems SHIELD could just scoop them up as they're heading to the bases nearest neighbor (which I imagine isn't close).
What SHIELD?
That would pre-suppose that 1) Anyone outside the Fridge even knew what was going on. 2) Weren't too busy dealing with the armed forces of various world governments coming to kick down their doors. And 3) anyone outside of SHIELD even knows the Fridge exists, let alone it's location. Hell even the guy that dose the super-imposed text isn't cleared for that info.

The chain of command has disintegrated, the infrastructure is in tatters and there are probably Hydra moles popping up everywhere, at all levels. It's pandemonium and Hydra are taking full advantage of the chaos and confusion while they can. Indeed that's clearly one of the reasons for the prison break, to keep what remains of SHIELD pre-occupied chasing down escaped super villains while they buy time to...do whatever it is they have planned.