In all likelihood there was no shadiness involved, but if there was, it will have been captured by AA's systems. As I understand it, AA employees are assigned different standby priority based on who they are (e.g., senior execs probably have the right to bump revenue passengers if they so choose) and why they are flying (e.g., a member of a flight crew that is needed at LGA to operate another flight will have priority). But an AA employee that is "just" commuting home will not have priority.

If you choose to write to AA, I would not alledge malfeasance. I would just ask them to look into whether proper procedures were followed.