I come from Pakistan where a lot of Shia say things such as "Moula Salamat Rake" or "Mola Shifa day" which means that it is the Imam who protects and it is the Imam who gives Shifa and not Allah. So many Shia say this and it is not considered Tawassul. Is this Shirk since the Ahlul Bayt are only intercessors through Allah and not actual wish granters like Allah?

As you mentioned in questions Ahlul bait (as) are intercessors and when a person is saying, if he means that Allah give through Ahlul bait as then it is correct.
All is based on niyat and intention.