Yes. There are general issues with the stated size of the bomb.
Scientific American even wrote up an article about it.
Early in Pacific Rim the plan to stop the kaiju invasion is revealed: Bomb the “breach” and destroy the inter-dimensional portal. To do this, the jaeger Striker Eureka is outfitted with a 2,400-pound thermonuclear device—equivalent to 1.2 million tons of TNT. That sounds impressive, but it is quite small in the annals of blowing up huge bombs. The largest nuclear device ever detonated—Tsar Bomba—was 50 times larger. Even so, the jaeger bomb isn’t anything to mess with. The energy it carried was about how much a large hurricane expends in any one second.
Size isn’t everything; depth matters too. Nuclear explosions have very different behavior depending if they are near the surface or deep in the sea. In fact, if you place a nuclear bomb deep enough, there will hardly be anything happening at the surface after it explodes. Maybe an upward rush of water, but no mushroom cloud. Conversely, if the bomb is only a few hundred feet under the water the resulting plume is absolutely incredible. So to find out what we’re dealing with in Pacific Rim we have to estimate the depth.
They go into the math, science and logistics and estimate that...
putting everything we could glean from Pacific Rim together, the jaeger bomb would create a bubble as wide as the Hindenburg—about 245 meters.
But the article is really about the plausibility of what is shown, with the Jaegers surviving the blasts and such.
The real question, however, is how much of a bomb was needed to destroy the Breach. Since the breach was really an unknown, it would have made more sense to go with as big of a bomb as possible.
However, since the Jaeger program was officially canceled months earlier, it is likely that they simply did not have access or funding for anything larger.