Nope. Apple's App store encryption is compatible with both GPLv2 and GPLv3. (A lot of people think the anti-Tivoization provisions in GPLv3 are not compatible with the App store. These people have not read GPLv3 carefully. The anti-Tivoization provisions are much narrower than they think).

The problem was with the TOS that a user must agree to in order to be allowed to use the store. The TOS places limits on the user that are incompatible with GPL.