I submitted a bug for ADAL js project (https://github.com/AzureAD/azure-activedirectory-library-for-js/issues/102) but would like to check with the community - maybe someone has insight on why it is so. Title pretty much says it all: ADAL js does not work in IE when acquiring token for remote endpoint when website URL is added to "Trusted Sites". I created two test webapps: webapp and webapi and published to Azure websites. These samples are based on https://github.com/AzureAD/azure-activedirectory-library-for-js/issues/102. WebApp: https://sergtestapp2.azurewebsites.net/#/Home, WebAPI: https://sergtestapi.azurewebsites.net. Anyone can try these apps out as long as you have microsoft account, because this app is multitenant. Once this question is answered I will wipe them out.
Pretty simple, navigate to WebApp and click login. ADAL js will handle the auth part and redirect to MS login page. Login -> navigate to "Go To List" and add couple items. Now, if you open IE or Chrome -> both "Go To List" should show the same items in the list. But if you add webapp to IE's "Trusted Sites" - you can longer "see/add to" the list in IE. Chrome would still work.