Actually no ships were ever under direct control of MacArthur, while at the same time all were...
What I mean is that the USN kept control of all ships, but they were under MacArthur's command..

In the battle of Leyte Gulf, during the invasion of the Phillipines, the USN lost several destroyers and 1 'jeep carrier' USS Gamber Bay of Taffy 3 ( 3 task groups of light carriers and Desroyers and Destroyer escorts were directly assinged to supporting MacArthur on the invasion beaches, named Taffy 1, Taffy 2, and Taffy 3) to Japanese heavy gunfire from cruisers and battleships, an additional jeep carrier, USS St. Lo to a Kamakazie and one medium carrier.. USS Princeton (pictured above) to a dive bomber
Excerpts from the battle below...
"At 0647 Ensign Jensen - the pilot of a plane from carrier Kadashan Bay - sighted, and then attacked, Japanese ships which he with remarkable accuracy identified as 4 battleships and 8 cruisers accompanied by destroyers.
Then, just before 7am, lookouts on the escort carriers saw the masts and fighting-tops of Japanese battleships and cruisers appear above the northern horizon. A minute later heavy shells began falling near Taffy Three.
The surprise was complete. Taffy Three was in a desperate situation, facing an exceptionally powerful force which also had a great superiority in speed over the escort carriers, while the only ships which Clifton Sprague had available to protect his flattops were the three destroyers and four destroyer escorts of his screen.
At 0657 Sprague had turned his carriers due east, begun working them up to their maximum speed of seventeen-and-a-half knots, ordered all his ships to lay smoke, and started to launch every available aircraft. At 0701 he issued a contact report and a call for assistance from anyone able to give it.
Japanese lookouts had sighted the escort carriers at 0644 when Kurita's ships were deploying from column into a circular anti-aircraft disposition.
Admiral Kurita then ordered "General Attack," permitting his ships' commanding officers to deploy against the US ships on their own inititative and without referring to the flagship. This was to mean that he lost control of the battle, and his giving such an order when his force was already engaged in redeployment caused immense confusion within the Japanese formation.
Shortly after the battle began Taffy Three's carriers entered a rain squall which protected them for about fifteen minutes and enabled Sprague to bring them around to the south-west - i.e. towards Leyte Gulf and the rest of Seventh Fleet.
At 0716 Sprague ordered his three Fletcher-class destroyers - Hoel, Heermann and Johnston - to counter-attack the Japanese formation. This they did with remarkable heroism and tenacity. They unflinchingly took on the battleships and cruisers, engaging these heavy ships with their 5-inch guns as well as their torpedoes.
At about 0750 the American destroyer escorts with equal heroism joined the counter-attack. At 0754 the vast battleship Yamato, now serving as Kurita's flagship after the sinking of Atago on 23 October, was forced to turn away for ten minutes by torpedoes from the American destroyers and was never able to get back into the action.
A very confused struggle by the DDs and DEs against the Japanese force continued for over two hours. By 0945 the Hoel and Johnston, and the destroyer escort Samuel B. Roberts, had been sunk by Japanese gunfire. At least one torpedo hit was made on Kurita's ships, and probably more, but what was of much greater importance was that the Japanese heavy ships had been forced into repeated evasive action and that this had slowed their advance, caused increasing confusion in the already badly disorganised Japanese formation, and deprived Kurita of any chance of regaining effective control of his force.
While the small ships of Clifton Sprague's screen were conducting these desperate counter-attacks the Japanese ships were also subjected to incessant assaults by aircraft from the three Taffies. Many of these attacks were carried out by aircraft armed with weapons intended for ground support and quite unsuited for attack on large warships, and many others were dummy attacks by unarmed aircraft.
Nonetheless, with the weapons available to them, the aircraft succeeded in sinking three heavy cruisers and damaging several other ships. These air attacks also played a vital role in support of the destroyers and DEs in distracting the enemy ships from the escort carriers, forcing them into evasive manoevres, and disorganizing the Japanese formation.
Despite all these heroic efforts the escort carrier Gambier Bay was eventually hit repeatedly by 8-inch gunfire, was crippled, and sank at 0907.
But then, entirely unexpectedly, and although his cruisers and destroyers were now on the verge of annihilating Taffy Three, Kurita at 0911 ordered his ships to break off action.
As Clifton Sprague later recalled -
"At 0925 my mind was occupied with dodging torpedoes when I heard one of the signalmen yell 'Goddamit, boys, they're getting away!' I could not believe my eyes, but it looked as if the whole Japanese fleet was indeed retiring. However, it took a whole series of reports from circling planes to convince me. And still I could not get the fact to soak into my battle-numbed brain. At best, I had expected to be swimming by this time."
While Taffy Three was fighting Kurita's ships, Taffy One was being subjected to the first organized kamikaze attack of the war. Later that morning Taffy Three itself was attacked by kamikazes. At about 1100 the escort carrier St. Lo was crashed by a Zero which caused a series of explosions, and she sank at 1125. Four more of the Seventh Fleet's escort carriers were damaged by kamikaze attack during 25 October."