I believe Common Markers are used to denote charges you have on certain cards, like your development cards. For example, as Geralt, when you pick a Potion development card, you need to use your Brew ability to place one charge on your Potion card, which is indicated by placing one Common Marker on it.
As you can see in the card text here, you need to spend one Charge (indicated by the Common Marker) in order to use this Potion card. All cards that require the player to spend a Charge start with 0 Charge (i.e. 0 Common Markers) by default, unless it is indicated otherwise in the card text.