I initially assumed it would be the IE that is currently installed but there seems to be some differences. I get JS related errors when loading my add-in Outlook 2016 Desktop but not in Office 365 (Web). How would I find solution to the problem if I do not know which IE is being used to render my add-in?
I found also some differences on the IE installed on your computer and the one running you add-in. For example, see the answer from Jeffrey Chen here he explains that the two IE do not run in the same integrity level (L-level vs M-Level).
I believe you may be interested in using F12 for debugging your add-in iFrame, see instructions here.