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.
Fridge Horror: The usual reason to do animal testing is to apply the results, if successful, to human beings. Let's hope the directors of NIMH are aware of the Scale of Scientific Sins.
Inferred Holocaust: The rats of NIMH increased from a group of 20 rats to 115 rats in only five years. Thorn Valley can sustain an estimated capacity of 2000 rats. If the rat population continues to grow at the same rate (about 142% a year), they will hit their maximum sustainable population density in only 8 years. Normally the fact that rats breed like... well rats, is remedied by predation and their own short lifespans, but since the rats of NIMH are too smart to prey on and they've been uplifted, their lifespans are many, many times that of an ordinary rat. These rats are either going to have to invent the world's tiniest condoms or the earth will be entirely overrun by hyper-intelligent rats in less than fifty years.
Rat biology may actually provide its own solution here, as males produce a jelly that literally blocks up the female's vaginal tract at the end of copulation. If Mr. Ages can concoct antidotes for spider venom, the rats should be able to synthesize an artificial "plug" for prophylactic use.
The sequels indicate that many of the mated Thorn Valley couples have limited offspring, and that many rats choose to focus on scientific pursuits for some years before even considering a family. Timothy and Racso's best friend Christopher often bemoans his only-child status.
Unfortunately, female rats that don't breed within the first several months of life develop pelvic fusions that can kill them during the birthing process if they're impregnated later on. Females that prefer work to motherhood might be better off having themselves spayed by rat surgeons.
Running the Asylum: After the death of her father, Jane Leslie Conly wrote two sequels for the original book. She was clearly a fan of the Don Bluthfilm because she incorporated movie elements that didn't exist in the original novel into the sequels, such as the cape Mrs. Frisby wears and Jeremy's somewhat more comedic personality. Other than that, though, the only real change was a POV-shift from the adult characters to the younger characters.