On the level '06', a boot can be found with a plant growing inside it in the missile control room. This is a reference to the movie Wall-E, in which Wall-E finds a plant and puts it in a boot.

In the level "Dead City", the creatures known as "Dark Ones" can be seen at various points throughout the level, watching Artyom. The first one can be briefly seen in the offices, the second one will cause a flashback when Artyom passes through the playground, and finally the third one is checking a corpse in the gated passage to the courtyard of the building Bourbon told Artyom to head to. Shooting one will get you a negative "moral point".