Basically Spencer went behind his boss’s back to try to cut a private deal. And, apparently lied about it.

Operative paragraphs from article:

Esper asked for Spencer’s resignation after learning that he had privately proposed to White House officials that if they did not interfere with proceedings against Gallagher, then Spencer would ensure that Gallagher was able to retire as a Navy SEAL, with his Trident insignia.

Spencer’s private proposal to the White House — which he did not share with Esper over the course of several conversations about the matter — contradicted his public position on the Gallagher case, chief Pentagon spokesman Jonathan Hoffman said in a statement.