I seem to recall the comic actually addressing that, but it's been a while since I read it.
Not to mention it's looking like 'Prometheus' might give the Company access to Aliens decades before 'Alien', let alone 'Aliens'.
It's not irreconcilable, maybe they had access to Aliens but didn't know what they were or didn't have concrete data, which would make Ripley's testimony in 'Aliens' seem really crazy. Special Order 937 seems to imply they knew something was out there, since they specifically put Ash on the Nostromo and then specifically sent it along the heading it was on. They may not have known it was Aliens specifically, and I don't recall Apocalypse changing that. If I remember right, Apocalypse had the Company with knowledge of the Jockeys, something which would jive with Prometheus anyway.
But seriously Apocalypse is like an Alien-centric proto-Prometheus comic -- explorers find evidence of an ancient civilization that had once visited earth, go out and explore and find one of the Jockey worlds, things go horribly wrong and almost everyone gets killed. The plots (as far as we know about Prometheus) are very similar.