If you are writing an academic paper that quotes from an author that uses the ellipsis in a way that differs from MLA style (such as the script of a modern play that uses “…” to indicate when a speaker is interrupted, or a graphic novel that might use “…” to indicate a meaningful silence in a speech bubble) my general advice is to remain true to the original source, while also not making it look like you are making a careless MLA style error.

This might mean avoiding the problem by paraphrasing a quote, or including a screenshot of a speech bubble. However, your professor probably wouldn’t want you to slow down your own argument to insert a digression about punctuation — unless, of course, your academic argument is actually about the punctuation.