it doesn't constitute a full plot hole.
How can you have part of a plot hole? It's either one or it isn't. As it stands, without an explanation, it makes no sense. Your making excuses for what is ultimately just bad writing. For a story that force feeds every plot point ad nauseum, I find it extremely suspect that Sakamoto chooses this one instance to leave it up to interpretation.
During the times she talks to Adam and he tells her about a weapon, how is she suppose to know it was the same thing she fought in Other M since she doesn't actually see the creature in Fusion until she finally fights it.
How is she suppose to... He calls it "Nightmare." Then, he describes what it is, what it does, and why it's so dangerous.
So you mean to tell me that Ship-Adam tells Samus all of that and her reaction would be, "Wha- Well, that could be
anything!" Other M creates a plot hole because these events are inconsistent and Fusion now blatantly disregards that Samus already knows what the Nightmare is based on Other M's place chronologically. Sakamoto goes out of his way to include this enemy in an attempt to tie the games together but he pushes them further apart.