There appears to be an inconsistency (or unpublished protocol) in many online hash generators when formulating a hash from an uploaded text file, versus strictly hashing the contents of a file. This issue appears to be unrelated to the name of the file, yet can be consistently replicated.
For example, hashing the following (by copy-and-paste at http://onlinemd5.com/)...
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. ... produces an MD5 hash of: A5E90C16BEB53BB93468496EAF2E0AC4.
Yet if one copies the above into a text file, then uploads the file, the MD5 hash produced is: 8F18B10192372D8523558CF65DB2B1B2, regardless of the name of the file.
In addition to the above site, this can reproduced at "passwordsgenerator.net/md5-hash-generator/" (copy-paste) and "md5file.com/calculator" (file upload), and is consistent among MD5, SHA-1, and SHA-256.
This implies that there are either unseen characters that are consistently being hashed within the file upload (independent of the filename) that are messing with the hash, or the algorithms are adding/subtracting characters upon file import (unlikely).
Why are these hashes coming out different?
I'm on a Windows machine, using basic notepad for file creation. Please excuse the "quote" links above; I do not maintain an appropriate reputation for multiple links in a post.