Taken from Wikipedia on Windows and Linux
However such an approach has indeed produced several vulnerabilities, although this is a rare case
Is that statement logically correct because it seems to contradict itself or am I just reading it wrong.
Indeed, considering the context:
Anyone with programming experience is free to fix bugs and submit them for inclusion in future releases and updates. However such an approach has indeed produced several vulnerabilities, although this is a rare case.
It could have been misunderstood to mean that "allowing anyone with programming experience to fix bugs" as a rare case, whereas in actuality, the sentence means "the vulnerabilities are rare cases, they do not happen often."
Yes, this sentence is ambiguous.
You're absolutely correct that the sentence could be better written, and other answers have given good suggestions.
If you're looking for a logical contradiction between several and rare, though, there is none. Several refers to the number of things (more than a few) whereas rare refers to a proportion of some population. If the population is large enough, than you can have rare things of which there are several: for example, several NBA players have been under six feet, but they are rare. In a very large population, rare cases can have even many instances: many people have eyes of different colours, but they are rare too!