Yes. This is a common and well-known glitch that has been occuring since the initial release of version 2.5, and has affected its updated versions. The latest version of 2.5 is 2.5.1, which was released on October 11th, 2011. If you have any version of 2.5, you will be affected by this issue.
Is there a way to fix this glitch?
Yes. There were multiple claims that killing your pups, then "re-loading" a previous save would solve the problem. I recently played the game and I found this to be somewhat true.
Here's how to solve the problem:
- Step 1: Get to the part where your wolf's pups are born. You may save at this point.
Step 2: Kill all of the pups. The easiest way to do this is by carrying each one individually and drowning them in the river. It may seem like starvation would be easier, but in my experience, your wolf's mate frequently leaves and comes back in time to feed them and prevent them from dying so long as you are in the vicinity of the pups. Although, if you distance yourself from them, your mate will be forced to stay with the pups until your return. You may be able to prevent feeding this way, but I haven't tried it.
Step 3: When the prompt appears after all of your pups have died, you are given two options. You can either re-load from a previous save, or restart from when your pups were born. Here's the difference from the claim -- choose to restart, and not to re-load. While I did not choose to re-load a previous save and do not know if it works, I had a feeling that re-loading from that first save after the brown pups were born would not change anything, and forcing a restart to the very moment they were born made more sense. Choosing to restart effectively changed the coat colors of the pups, and yes, the coat colors reflected the colors of the actual parents.