The Cyprus Agency uses a white dandelion with a few seeds parting from it as its logo. This makes a terrifying level of sense at the end of the episode when it turns out that the CEO and founder, Owen Mallory, fathered the children provided by the agency himself. Just like the white dandelion, he has provided plenty of seeds that have been scattered everywhere and grown.
Red proceeds to give the Cabal all of the massive world changing Reed Richards Is Useless averting inventions stolen by The Lindquist Concern. Which goes a long way to making up for the Cabal's losses to Reddington over the past few years. It also means they'll be making billions in technology through (mostly) legitimate reasons.
Liz successfully captures "Lord Baltimore" a.k.a. Nora Mills. Yay! Except, the "Rowan" personality still exists inside Nora and. as Liz points out, the two personalities weren't aware of each other and therefore could not have been conspiring to cover up Nora's crimes. That means that Rowan is basically an innocent victim of Nora's criminal empire. Now consider that anything could potentially wake up the "Rowan" personality: She could find herself in a federal prison, having no clue why she's there and completely at the mercy of her fellow prisoners. (Since Rowan, unlike Nora, is not a hardened criminal).
Karl Hoffman (The Good Samaritan Killer) inflicts the same injuries on his victims that they dealt out to the targets of their abuse. When his mother is seen crippled in a wheelchair, unable to speak, and with a disfigured face, one can only wonder what pain she inflicted on her son, and how sadistic Hoffman was when exacting his retribution.
In Season 3 Episode 6, Solomon and Reddington have a firefight in the part of Crispin Crandall's plane where the kidnapped frozen scientists (via cryogenic preservation) are kept. A lot of the tanks are damaged by the shoots. So... What happened to the people frozen inside? It's easy to assume that the system keeping them alive has been damaged too...
Red says they're not cryogenically suspended. Red says they're dead and frozen. I.e. pointing out the euphemism for current cryogenics often overlooks this part. The entire plan depends on the idea of reviving deceased scientists in the future when that technology is unlikely to occur without the geniuses he's killed—if ever.
In Season 2, Episode 9, "Luther Braxton," a special network connecting the Pentagon and various intelligence agencies is routed through a blacksite prison on an oil rig, and it was taken control by Braxton who is holding various government employees hostages, demanding the codes to access the network. This would give him access to all of the intelligence assets and the ability to compromise them. Why this is unlikely: the site is on an oil rig in the middle of the ocean; either it's connected by cable/wire/optical fiber, or it's connected by some form of radio (shortwave, longwave, microwave or satellite), or both. Either cutting any wire to the facility or jamming all radio signals (or both) would isolate the site from the network and it would not be able to communicate with anywhere else, whether or not it had the codes.
How did the woman at the beginning of 'The Cyprus Agency' escape? Even if she woke up, she'd been in a coma for a long time. Also, why did nobody notice a police officer was shot?