I faced an issue in the step-by-step simulation of a non-deterministic PDA.
After choosing the desired transition (the a-transition at state z0 in the below SSCCE) the word stack is not pushed down, respectively the stack pointer is not increased, even though the transition defines a read operation. This misbehaviour also affects the correctness of the overall results, i.e. the PDA does not accept words which it technically should and vice versa.

I already dug into the source code (branch trunk) and from what I can tell the method AbstractStateMachine#nextSymbol(Transition) is missing a this.word.nextSymbol() somewhere. Unfortunately, I faced some problems to get the project built properly and therefore I cannot send you a patch or PR.