When a team gets extra points or penalty point for whatever reason, you can enter this at two locations:
"Matchdetails" window (specific match)
Select at the "results" page the correct match and open the "matchdetails" window.
At the upperleft and upperright are 2 spinners for entering extra points (+) or penalty points (-).
At team which has got penalty points or extra points has an asterix (*) after its name in the standings.
Under the stingstable is text for explaning the asterix. See settings to modify this text.
"Settings", "Current league" (general)
Just enter the correct values for each team at the right.