In most cases the error occurs after you jailbreak your iOS 6 using Evasi0n or such. But wait the minute that doesn't relate to compatibility between iOS 6 and Evasi0n tool, neither there is a hardware damage on your iOS device.
The error is simply because the regulation Cydia have set for the maximum number of source packages a user can add to their device. Currently we can only collect 65.535 packages at maximum on our iPhone, thus if you go beyond that limit, you will be facing that error.
To be clear the error comes with three lines, but the main culprit is the first one, which is saying.
Error Cydia wow, you exceeded the number of package names this APT is capable of.
So how to fix it?
Thank God! It doesn't take a magical formula to fix it. Since it's all about "capacity", then all you need to do is delete the most unused packages installed on your device by going to:
Cydia > Manage > Sources > Edit.You will see a list containing the packages installed, therefore delete ones you rarely use. But don't delete default sources like BigBoss, Cydia, ModMyi, Dev Team, etc.
That's how you fix that Cydia error. Hope you found this post useful. Cheers.