If a creature has +1/+1 counters and -1/-1 counters on it, state-based actions remove the same number of each so that it has only one kind of those counters on it. For example, if a creature has three +1/+1 counters on it and two -1/-1 counters are put on it, state-based actions will remove two of each of those kinds of counters, leaving the creature with just one +1/+1 counter.