Harsher in Hindsight: Alex laments bitterly that his parents wanted him gone, and that if he were to escape and see them again that they would try to get him sent back to prison. However, it is revealed in Execution not only have Alex's parents died, they originally tried to reppeal his life sentence seven times, leaving a note behind that asks Alex for his forgiveness.
Ho Yay - Unavoidable to the point that the characters know it themselves. In Lockdown, Alex became startled when Donovan started stripping seemingly randomly once they were both alone, and D joked, explaining it was because he loved Alex (it was really part of an escape plan). Same joke was used when Alex got rid of clothes near Zee two books later. The Skulls call Zee Alex' girlfriend, and hugs and touching and I'm-so-happy-I-can-kiss-you abound - some kissing actually happens, with Simon kissing Zee's forehead.
Foe Yay - The first half of Death Sentence is drowning on this. The warden calls Alex his, raises his head by holding his chin, touches him a lot and sits together with him in bed, talking to him with a gentleness Alex knows to be genuine. All of that more than once. And because of the nectar, Alex is prone to view the warden in a positive light and becomes happy like a puppy whenever he gets praised. Alex recalls this in Fugitives with an "I almost gave myself to him".
Name's the Same: Both unintentional happenstances regarding two leaders of the Skulls:
Kevin Arnold, who Gordon admits he accidentally gave the same name as Fred Savage's character on The Wonder Years.
Gary Owens, who shares the same name as real life voice actor Gary Owens.
Portmanteau Couple Name: The ship name for Donovan and Alex is "Donovalex", whereas the ship name for Alex and Zee is "Alzee".