We develop a technique that uses pebbles in a very economical way for simulating a multi-counter automaton on a sequence of input strings and maintain a count of those strings accepted by the counter automaton. Based on this result we show the failure of a previously proposed method for constructing witness sets separating classes of languages accepted by pebble automata with an increasing number of pebbles. We also give a recognition algorithm for another family of languages suspected to separate the lower levels of the hierarchy.