Three reasons working together:
The weakpoints haven't impacted survival
There are plenty of animals in nature with obvious weaknesses that would perhaps even be easy to exploit. But if the species still exists, it must mean that these weaknesses are not critical: even if one, two or twenty specimens end up crippled or dead because of the weakness, the situation is such that the species is able to go on: the damage happens sporadically enough that enough members are able to carry on the genes to the next generation.
Perhaps the weakpoints they have are not exploited by the fauna of their environment: evolution wouldn't "notice" something that doesn't threaten survival systematically. If the weakpoints are exploited, it doesn't happen on a large enough scale to matter.
Evolution is always ongoing
Evolution is not ever a settled matter: species evolve continuously, and over very long periods of time. Perhaps what makes the weaknesses weaknesses is a relatively new danger, introduced to the environment too little time ago to have any impact on evolution yet. 335
Perhaps the weakpoints will be gone eventually, or perhaps they will not matter enough to be ever gone. Relying on evolution is not a good short-term survival strategy: perhaps the species will be wiped out far before the weakness could be eliminated by evolution.
Large creatures have significantly more cells, many orders of magnitude more than small ones. This makes natural evolution slower, especially if they are hard to kill: the less advantageous genes are not disadvantageous enough to allow or trigger a cull, and so they carry on.
Exposure to magic could accelerate mutation: that accelerates evolution, but, similarly to radiation, it's random and has no will of its own: no interest in creating mutations that are "good" or "useful": some could be weaknesses. Large creatures are more resistant to averse random mutation because their larger number of cells makes sure the probability of something bad being developed are much lower, but this is also true for positive things.
The weakness balances the species' population
Being able to reproduce without any hindrance is not an unconditionally good thing for a species: when too many individuals cohexist at the same time in the same place, resources become scarce, and this can lead to extinction if the lifespan of the creatures is long enough that there would be no time for the environment to recover by the time the surplus starves.
This is especially true for apex predators and very large creatures, since their survival depends on, respectively (but not exclusively), a healthy population of prey and very large amounts of resources.
A critical weakness that menaces in the environment can only exploit occasionally would help reduce population in the short-term, helping the environment resist the foraging by the large creatures enough that all can survive.
Disclaimer: I just like the topic, I'm not a biologist and I reported facts and expectations as I remember them and as they make sense to me, but my assumptions could very well be wrong. 238