The Yellow Squares on the Mission Map are considered to be "Extraction Points", except that some of them may be declared to be something else by scenario descriptions. Some Extraction Points are at the same time Deployment Points; it is typically chosen at the start of a Mission which Yellow Squares are Deployment Points, and sometimes, scenarios may in part or in full make that choice in advance.
Extraction Points that weren't chosen as Deployment Points and that doesn't have any other special Mission function can be destroyed by attacking them and dealing either two normal damage or one CRITICAL HIT damage. This is mainly a way for the Overmind Player to prevent the Hero Players from using them as Extraction Points. (There is also some Hidden Agenda card that rewards the Overmind Player for destroying Extraction Points.)
Yellow Square
The Mission Map in Chronicle X is made up of Map Tiles which each has a grid of five by five Squares on it. Some of those Squares have a highlight colour, and the ones that are highlighted in yellow (and has an arrow icon on them) are potential deployment spaces, where either the Hero Players or the Overmind Player can place their Models (or Blip Tokens, in the Overmind Player's case).
Note: which of the Yellow Squares that are actually deployment spaces is chosen at the start of the Mission. After that, the other Yellow Squares can usually not be used for deployment, although they can still be used by some abilities that specifically refer to Yellow Squares.