On 8 April 1942, an aircraft identified by Mackerel′s crew as a United States Army Air Forces P-38 Lightning fighter mistook Mackerel for a German U-boat and dropped four bombs which straddled her track while she was conducting exercises with the U.S. Navy patrol vessel USS Sapphire (PYc-2) 3 nautical miles (5.6 km; 3.5 mi) south of the Watch Hill buoy off Watch Hill, Rhode Island.

[8] A subsequent investigation of the incident by the Eastern Sea Frontier found it impossible to reconcile the reports of the two vessels and concluded that Mackerel had mistakenly fired a torpedo at Legare.

[9] Continuing her voyage toward Norfolk alone after losing contact with Legare, Mackerel again sighted a U-boat at 05:08 on 15 April 1942 near the entrance to the Chesapeake Bay.

[9] At 09:50 on 4 May 1942, she was operating off the coast of Rhode Island when the American tanker El Lago sighted her and mistook her for a German U-boat, and El Lago′s United States Navy Armed Guard detachment opened gunfire on Mackerel about 4 nautical miles (7.4 km; 4.6 mi) south of Watch Hill Light at 41°18′N 071°47′W / 41.300°N 71.783°W / 41.300; -71.783.

[10] Mackerel sustained no damage, and did not require assistance from two U.S. Navy patrol boats and a United States Army tug sent to her aid.

The 1943 World War II submarine movie Crash Dive, starring Tyrone Power, features footage of Mackerel′s sister ship USS Marlin (SS-205) portraying the fictional U.S. Navy submarine USS Corsair, with her conning tower modified to resemble that of Mackerel.

A fictional submarine named USS Mackerel that fought in the Pacific during World War II is featured in the 2005 novel Pride Runs Deep by R. Cameron Cooke.