They kept saying the generators for the hospital would only run for 48 hours. They did this to add tension. But Generators are made to last weeks. When fuel runs low you just add more.
In this episode the character of Ian Lim is seen carrying a sidearm. Lim is an analyst and FBI Analysts do not carry guns.
The surgeon for Valentine's son says they can't operate because the malware has them locked out of their blood bank. However blood isn't stored in some kind of impenetrable vault, plus there would be a way to manually open the doors in the event of this very situation.