The issue I see is that when I go inside the project (e.g here https://github.com/krzyzanowskim/CryptoSwift/tree/master/Sources/CryptoSwift/AES.swift) a copyright notice is displayed.
That's fine. It is usual for the author to retain the copyright while licensing the work under to others under a permissive license. The fact that the code has been licensed does not undermine the author's copyright ownership in any way; for example the author is free to license the code under other a proprietary license as well.
The phrase "all rights reserved" does not contradict the licensing of the software. In the past this phrasing was required to claim copyright in some jurisdictions; today it has no legal effect because copyright is automatic in most legal jurisdictions. Thus at most this phrase means that copyright is being claimed, not that that particular file is not being licensed under the project license.
More specifically, the "rights" that are being "reserved" are the property rights in the copyright itself. It's a little confusing because without knowing the legal history a layperson might well assume that "all rights reserved" means something like exclusive distribution; it does not.