Calling remove on a collection while you're iterating through it will cause a ConcurrentModificationException every time, even if it's all done in the same thread - the Right Thing to do is get an explicit iterator and call .remove() on that.
Edit: Modifying your example:
Iterator> i = eventMultiMap.entries().iterator();
while (i.hasNext()) {
if (i.next().getValue().equals(command)) {
i.remove();
nbRemoved++;
}
}