One of the biggest problems with mega-threads in a technical one. When threads are merged into a mega-thread, a ghost post is left to show that a thread has been merged. However, clicking on that post, takes you to the first page of the mega-thread, not to the merged post itself. So even if you are interested in the original post, you have to go search for it within the mega-thread.

Mega-threads also making searching difficult and less efficient, as original posts usually have more specific titles, that are then lost when they are merged.

Also mega-threads that span many months often have out-dated or incorrect information as programs change and evolve.