Plot hole: When Hulk and Banner have been physically separated by the nutrient bath, they are both wearing tattered pants. Given that Hulk and Banner were previously occupying the same body, this should not be possible. Hulk was the one that went into the nutrient bath, so if Banner's body was separated from Hulk, then Banner should be naked.
Continuity mistake: When Jennifer Walters is first introduced, her fingernails are unpolished. Later when she is restrained in Dr. Doom's lair, her fingernails alternate between being painted pink and red. Given that she and Bruce were running for their lives, she wouldn't have had time to paint her nails. Later when she transforms into She-Hulk, her fingernails turn green with the rest of her body, but if her fingernails were painted, they should still appear that color, as her skin and hair turning green wouldn't magically remove nail polish.
Factual error: When the Hulk jumps up and grabs on to the tail of the helicopter, he is somehow able to hang on to the tail while spinning the helicopter in a circle. Helicopters require a certain weight distribution in order to maintain stabilized flight. Someone of the Hulk's size and strength wouldn't be able to just hang on to the tail and spin the helicopter. He instead would bring the helicopter crashing down.
Plot hole: This series is in the same continuity as the other Marvel animated series that aired around the same time - X-Men, Spider-Man, Iron Man and Fantastic Four - by virtue of each aforementioned show crossing over with at least one of the other shows. However, the origin of the Leader in this show is inconsistent with his origin in Iron Man. In the Iron Man episode "Hulk Buster," which originally aired on February 10, 1996, Samuel Sterns became the Leader after a barrel of gamma waste fell over and spilled its contents onto him. In this show, which didn't air its first episode until September 8, 1996, Samuel Sterns became the Leader after he sabotaged Bruce Banner's gamma bomb test and fell into a pit of radioactive waste caused by the bomb. Rick Jones' role in Banner being exposed to the gamma bomb is different as well. In Iron Man, he parks his jeep in the test area and casually plays a harmonica. Here, he is riding his motorcycle through the test area and crashes, and is unable to restart his motorcycle in order to get clear of the blast.
Plot hole: After Dr. Doom's robots abduct Jennifer and load her into the aircraft, Hulk hitches a ride all the way to Doom's estate, falling off the aircraft and breaking into the estate before the aircraft has time to land. Despite this, Dr. Doom already has Jennifer secured to an infirmary table and medical machinery by the time Hulk confronts Doom.
Plot hole: This series is in the same continuity as the other Marvel animated series that aired around the same time - X-Men, Spider-Man, Iron Man and Fantastic Four - by virtue of each aforementioned show crossing over with at least one of the other shows. However, the portrayal of Sasquatch between this show and X-Men is not consistent. In X-Men, Sasquatch was a mutant and longtime member of Alpha Flight, under the purview of the Canadian government. In this show, Walter Langkowski is a hermit that had only recently become Sasquatch through a gamma experiment gone wrong, and he chooses to exile himself into solitude by episode's end.
Continuity mistake: When Bruce is rappelling down the shaft, at one point he turns his body face down, and you can tell by the rate at which the background is passing by that he is instantly going slower than the previous shot. If anything, his speed should have increased since he's no longer in a position to slow his descent by using his hands to rub against the rope.