IIRC he didn't specifically say Magneto helped build the "first" cerebro. Indeed from the context of the conversation it seems as though he's talking about the modern one they were standing in at the time. Of course that conversation would also pre-suppose that this is the only cerebro, but I don't think the retconned existence of an early prototype matters one way or the other.
Maybe in DoFP we will see Erik help Xavier build the one under the mansion. Indeed, with all the seamless metal lined corridors, it's more or less implied that the whole thing was built by Magneto.
As for their ages when they met, yeah, that's an inconsistency, but a fairly minor one IMO. They were still both young men at the time and very different people and I doubt the average viewer is going to remember that precise detail mentioned in passing. I know I didn't.
The multiple Emma's are easily dismissed as co-incidence, but the two Moiras area little more problematic because of their connection to Charles. I suppose one could be the daughter of the other (I forget how old the actress was in X3?) or we could suppose that Agent MacTaggert retired from the Agency and became a doctor? But that might be pushing it.
Anyway, this is all minor niggling stuff, of a sort that the comic are just as guilty of, so I don't see it as a major issue.