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I am reading the book "Shattered Sword" and it states that Yamamoto "rebuked" Nagumo after Pearl Harbor. I thought Pearl Harbor was considered a great success? Anyone know why Yamamoto thought it necessary to reprimand Nagumo? TIA

Essentially for failing to carry out a third attack. Wikipedia (my emboldening):

In the end, five American battleships were sunk, three were damaged, and eleven other cruisers, destroyers, and auxiliaries were sunk or seriously damaged. The Japanese lost only 29 aircraft, while 74 were damaged by anti-aircraft fire from the ground. The damaged aircraft were disproportionately dive and torpedo bombers, seriously impacting available firepower to exploit the first two waves' success, so the commander of the First Air Fleet, Naval Vice Admiral Chuichi Nagumo, withdrew. Yamamoto later lamented Nagumo's failure to seize the initiative to seek out and destroy the US carriers, absent from the harbor, or further bombard various strategically important facilities on Oahu. Nagumo had absolutely no idea where the American carriers might be, and remaining on station while his forces cast about looking for them ran the risk of his own forces being found first and attacked while his aircraft were absent searching. In any case, insufficient daylight remained after recovering the aircraft from the first two waves for the carriers to launch and recover a third before dark, and Nagumo's escorting destroyers lacked the fuel capacity for him to loiter long. Much has been made of Yamamoto's hindsight, but, in keeping with Japanese military tradition not to criticize the commander on the spot, he did not punish Nagumo for his withdrawal.

which suggests the criticism may have been somewhat unjust.

The "strategically important facilities" included fuel stocks:

Wikipedia:

he was later criticized for his failure to launch a third attack, which might have destroyed the fuel oil storage and repair facilities. This could have rendered the most important U.S. naval base in the Pacific useless, especially as the use of the submarine base and intelligence station at the installation were critical factors in Japan's defeat.

Because Yamamoto was one of the few admirals in the Japanese fleet that understood the importance of logistics. Other Japanese admirals, such as Nagumo, measured their success by the damage to enemy warships.

Specifically, Nagumo was satisfied with his two strikes, which blew apart the battleship USS Arizona, and severely damaged all but one of the other seven American battleships. That put the U.S. Pacific Fleet out of action for some time.

But Yamamoto wanted Nagumo to make a third strike to destroy the fuel supplies and dock facilities. That would have done more damage to the American Pacific effort than the loss of its warships.

Yamamoto also reproached Admiral Mikawa, who won a victory at Savo Island, for the same mistake. Mikawa sank several allied cruisers with a midnight surprise attack, and then left the scene. But Yamamoto faulted Mikawa for not destroying the Allied transports, with their supplies and reinforcements.

Yamamoto understood better than other Japanese admirals that the whole purpose of defeating enemy warships was to earn the right to destroy their "soft" targets. The other admirals felt that sinking enemy ships was "enough."