Groves made a lot of enemies throughout his career, and Eisenhower's gripe with him in 1948 was not about whether he did a good job in 1945, but whether he was doing a good job in 1948. By 1948 he was running the Armed Forces Special Weapons Project, a very different sort of organization than the Manhattan Project. With the Manhattan Project, Groves had the ability to essentially be a minor dictator of his own secret agency — he was insulated from criticism and audit, and had the coveted AAA priority rating that allowed him to requisition whatever resources or people he wanted without being significantly challengeable. His style of operation was very well-suited to the conditions of the Manhattan Project, where he was able to bulldoze his way towards a very specific outcome. It was extremely ill-suited for the postwar, however, because the outcomes were more nebulous, his authority was not absolute, and his oversized ego had become resented by other military brass who considered him to be perhaps a bit too big for his britches. He wasn't some kind of war hero in the sense that Eisenhower or MacArthur was — he was an engineer that managed an industrial production project.

Despite all this, Groves had some supporters in the Senate, and some in the military. But he had a huge list of enemies, including David Lilienthal, the head of the Atomic Energy Commission, and the scientists on the General Advisory Committee secretly regarded him as a hinderance in transitioning the atomic weapons business from its "crash" wartime footing into something more regular and systematic in nature.

Groves and Eisenhower never got along, ever. Their styles didn't mesh, their personalities didn't mesh, and their experiences didn't mesh. Eisenhower's specific complaints were almost exclusively about these kinds of things: Groves was rude and ruthless when it came to other officers who he felt were standing in his way; he was arrogant; he was single-minded in his attempt to accomplish his goals, no matter who got in the way; he did not abide by rules; he repeatedly worked to achieve advancement through tricks rather than by putting in the "dues" that were required of others. And — perhaps ironically — he was too young to be the Chief of Engineers, and so there weren't a lot of positions actually open to him for advancement at that point, and it was an "up or out" situation regarding promotion. The people Eisenhower wanted to promote, in any event, were the commanders who had succeeded in Europe and the Pacific — not those who had stayed on the home front.

All of which to say, there is a classic truism that says that Churchill was a great Prime Minister for war, but a terrible Prime Minister for peace. One can debate that particular example, but Groves was a great project manager for war, and the Manhattan Project probably wouldn't have been a success without him. But those particular qualities that made him good for a "crash" program made him awful for the day-to-day of peacetime operation, and he showed himself totally unwilling and unable to adapt to the culture clash that existed between him and the combat commanders who were going to be running the show in the Army for a long time. The very things that made Groves successful in 1942-1945 made him fail in 1947-1948, to put it very simply, because the context of the latter was very different than the former. It is of note that much of the Manhattan Project's operations underwent many transitions in this time as well; Norris Bradbury was a very different sort of manager and scientist than J. Robert Oppenheimer.

The best biography of Groves is Robert Standish Norris' Racing for the Bomb, and the specifics of Eisenhower's complaints that I've given come from chapter 25, which goes into great detail on the specific circumstances that lead to Groves' retirement.