Hey 

West Jerusalem is undisputedly in Israel, thus the "Mosques in Israel" category is correct. However, East Jerusalem is not under palestinian sovereignty in any way. That is the consensus here on wikipedia and in the international community. It is indeed considered to be occupied by Israel but not under palestinian sovereignty. It is located in disputed territory and it would therefore be a POV-push to write it is under palestinian sovereignty. Wikipedias consensus on all relating articles is that it is disputed and neither in Israel or the palestinain territories. For example Al-Aksa Mosque. Disputed is NPOV.