I am having issues when trying to delete a custom milestone from NPD.
I click on the red "X" when in edit mode, but the row remains.
I am using:
Wed 02/12/2014 041
with IE 11, running in compatibility view (Document Mode 5)
I have one IE11 client running in compatibility view(Document Mode 5) and was able to delete Custom Milestones in NPD project template.
Can you help verify whether you can reproduce it using another client?
see whether it works after cleaning your cache in your browser.