jQuery, prototype, MooTools and other javascript libraries sometimes have conflicts with each other.
Right, but Active Forums doesn't use any javascript libraries other than our own which is properly encapsulated in our own namespace. Unless another namespace is amaf.UI, amaf.Utils, etc I'm not sure how would conflict.
A common problem I have seen related to many javascript libraries is how and when they are loaded. If something affects the dom (AJAX) or another error does occur then it could prevent the library from loading properly or functioning as it should.