To start with, your naming convention is off. The size() of a List is... the actual size. If you want to reference the last index then your variable should reflect that.
You should also be using the $math.sub method, since the subtraction - operator is not actually supported (it only works in your case because the parser sometimes lets it through; it will not work if you use $a-$b without a space, for example).
So a more semantic & less fragile version of your code is:
#set( $lastIndex = $math.sub($Course_Enrollment__cList.size(),1) )
#set( $lastCourse = $Course_Enrollment__cList.get($lastIndex) )
$!lastCourse.Course_Offering_Product_Name__c
Now, to the question of output. You should only be testing Velocity-powered emails using either [a] preview-by-list or [b] a real email, never a sample. The sample can have little to no resemblance to the real-life result. Similarly, you need to check in both Batch and Trigger campaigns (if you might use both to send the same email) as the results can and will differ!
To debug this further, you should begin by outputting the entire $Course_Enrollment__cList in an email. Prematurely suppressing a possibly-null property (with the $!) makes things much harder to track down.
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