Minor Plot Hole: So over all the years of knowing the inter-dimensional rift exists, no one has ever figured out how to send anything through to the other side until two scientists manage to techno-mind-meld with a Kaiju fetus and learn the rift only opens if you have Kaiju genetics with you. However, not only do the Shatterdome's communications and sensors still track Gipsy Danger when she falls through to the other side, but Raleigh's escape pod somehow makes it back through the rift alone.
Minor Plot Hole: So the Kaiju Leatherback sets off some kind of EMP that instantly knocks out all of the Shatterdome's electronics, communications, and even one of their super-expensive and super-high-tech Jaegers. But fortunately, the several dozen helicopters necessary to transport Gipsy Danger into battle are mysteriously unaffected.
Major Plot hole: So the world governments are retiring the Jaegers because they cost too much and the Kaiju are getting stronger and stronger, and instead their plan is to... build a huge-ass wall around the entire Pacific Ocean. Setting aside that this plan would almost certainly be way more ridiculously expensive than the Jaegers, how exactly is this a long-term solution? Are the world governments basically planning to just let the stronger and stronger Kaiju mass up in the Pacific and just hope their walls hold forever? Their plan is so stupid it almost feels like the movie's writers wanted to make it clear that Marshall Pentecost is the last competent person on the planet.
Plot contrivance: When a nuclear reactor melts down, it does not result in a nuclear explosion. Yes I know it’s a giant robot movie but nowhere in the premise of the movie is it clearly stated that nuclear reactions are different in Del Torro’s world. Hence – shut up.
Plot contrivance: Why pick up objects made of lesser metals to hit monsters with rather than punch them with your super rare-metal billion dollar alloyed fists? It’s like a 200 pounds muscle guy who decides to grab a bag of Cheetos and hit you with it as hard as he can instead of punching you directly in the face. Looks cool – still dumb.
Plot Contrivance: The beginning exposition makes it clear how important a close bond based on common memories is between the Jaeger pilots, and that this bond is extremely rare - so rare that having it is enough to overlook other obvious personal and professional flaws. The introduction to the original pilots reinforces this - pilot crews are brothers, triplets, father/son, and whatever the stereotypical scary Russians are. However, as soon as the plot requires Raleigh to have a new partner he apparently instantly forms an extremely rare instant life bond with Mako, who he knows nothing about except that she's hot. Plot hole, or subtle social commentary about gender politics? You decide.
Unaddressed Issue: To fight the Kaiju, humanity's best option was to build hugely expensive and resource-draining gigantic killer wrestling robots to beat them to death in hand-to-hand combat far off the coasts of major cities. Then, in the movie's ultimate fight, we also learn that apparently nuclear weapons are also pretty effective against level 4 Kaiju and lower. I mean, building gigantic super-robots is cool and everything, but why wouldn't the world's governments just nuke the hell out of the Kaiju as soon as they detected them in the middle of the Pacific Ocean? Are they worried about pollution or something?
Unaddressed Issue: So. For years the scientists have known that the monsters can only come in through one single portal, and at one point Earth had around 30 Jagers spread out across the the world, so why not concentrate all 30 of these giant killing machines AT the portal to gang-bang on the monsters as soon as they emerge?