The reason they didn't call him up was correct, they wanted him to stay with his club for the playoffs. The problem was communicating it, and with all the influx with US Soccer at the moment, it's very easy to see how something like that would fall through the cracks. Who's responsibility is it to do something like that? Probably the manager, and the interim manager really doesn't the power/authority to say how he'll be used in the future. Why would he go out of his way to help out the next guy that will get selected for the job.
That's why they probably should've had an agreement with Arena to stay on-board, keep things stable, until everything else got sorted out. Basically no one realized it was their responsibility, and no one did it in the end. I wouldn't call it incompetence, just a consequence of having everything influx.