These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Critical Research Failure: There's a few of these scattered throughout the books, with the most egregious ones appearing in Atlantis Found and Trojan Odyssey.
God-Mode Sue: Name a protagonist or major good guy. Now try to name a single time they genuinely put a foot wrong or made a bad decision. To Cussler's credit, Rule of Cool makes this somewhat forgivable, but...
Iceberg. Hunnewell's death. Pitt spends a good portion of the rest of the book angsting about whether he did something wrong.
There's also his failure to prevent Maeve's death in Shock Wave.
Cyclops. Pitt agrees to help the one who insulted him for no reason (and no reward has been promised for his help). Leaves himself entagled in the flight to Cuba plot although he fully understands there's something fishy involved, because he is so tempted to search the namesake vessel he disregards safety.
Inca Gold. Pitt dives alone (which is not allowed by rules because it's too dangerous) in the sinkhole, finds his pals abducted and himself left to die in the water. Shoots the private parts of the aggressor, but leaves him alive to seek revenge later. Searches the Sea of Cortez with a very small team and no armed guards although he knows which kind of bastards are around. Flies the NUMA helicopter to the treasure mountain with most of the team leaving the ship unguarded and his crew and lover unarmed. Knows in which miserable physical state he is when he swims in the treasure cave, but wastes time taunting the criminals instead of shooting them on sight. He does all the imaginable mistakes, but his sheer badassery allows him to gain victory in the end.
Harsher in Hindsight: Most notably the plot to level half of Manhattan, outwards from the World Trade Center, which was thankfully foiled at the climax of Valhalla Rising.
Values Dissonance / Fair for Its Day: One subplot of Iceberg (1975) involves Pitt pretending to be Camp Gay to get a potential enemy to underestimate him. Sandecker even asks him why he's acting like a "faggot". Incidentally, the foe in question is a homophobe (and a domestic abuser, and a Corrupt Corporate Executive, and a megalomaniac) and Pitt guessed that he would be when they met based on his personality. When Pitt reveals the truth, it's in the middle of beating five types of crap out of him, which is payback for the beating he got from him earlier, where he didn't break character. Also, he seems to have no problem with Kristjan becoming Kirsti, and is more concerned with the fact that she seems to have become a sociopath.