He made a power grab and got called on it.
He attempted to consort with a foreign government to subvert the constitution of Honduras and conduct an illegal election. When the national board of elections refused to go along, he tried to fire them. He then told the country's supreme court to take a hike. The military was acting under orders of the Honduran Supreme Court when they removed him from power.
Had it been a military coup, there would be a general sitting in the president's office instead of the head of the honduran congress as stipulated by honduran law.