Hi Sam,
Doing repair disc permissions, normally should not create problems, reason being this is Apple's own built-in utility.
I am guessing there might have been permission issues already on your computer and repair disk permission tried to resolve that problem. But if the problem is severe these things may happen.
I would suggest you first you may try it again if that didn't resolve you should contact Apple support. They may help to repair the permissions.
~Ajlan Huda.