This is called lag compensation. Lag is a term indicating the tendency for delay of a particular Internet connection.
More lag means a longer time is required for a player's moves to be communicated to the game server, which can make it seem as though the player is moving somewhat more slowly.
The difference is not usually very important for standard chess games but can have a big effect on blitz and bullet games. Because of this, the game timer takes relative amounts of lag into consideration when determining how much time a player actually took to move.