Do counters combine? Can three +1/+1 counters be considered one +3/+3 counter?
If three +1/+1 counters are placed on an object, that object then has three counters on it. Animation Module's second ability can only put one additional counter on it each time you activate it. The counters do not change type, so they are still +1/+1 counters, and that is the only type of counter you can give it another of.