Blue Squares on the Mission Map mark places where Spanner tokens are placed at the start of a Mission. The Blue Square has no game effect after that, but the Spanner token has, as long as it's there.
Spanner
Spanner tokens are used to mark unidentified Items on the Mission Map. Spanner tokens are placed on all Blue Squares on Map Tiles during Mission setup.
Spanner tokens are not obstacles. Both Heroes and Alien Units can stand on a Square with a Spanner token, and when it does, it can use an Interact Action to pick up the item; to do this, spend the Action, discard the token, and draw an Item card from the bottom of the Item deck. (Draw from the bottom because some of the cards are double sided.)