Being as I already had X-Com: UFO Defense from many years ago (that I used to run via both DOSBox and through UFO Defense Extender) I thought I'd go checking up on the files I used to use to compare with the GOG version that I've just bought this evening (yes, it was an instabuy).

Now, one file I did find was an archive containing "fixed files". The only information I could get from the "read me" files is that it was a fix directly from Microprose Europe for the Y-axis error.

If I can find an online resource for it I'll update with a link, but does anyone remember what this fix was about and whether the GOG version already contains it? Going through the archive's files, all it contains are replacement game files (.MAP and .RMP files).

Well, I can't find any online resource for it any longer, so I've no idea where I originally got it from all those years ago. However, having looked at OpenXcom, that also has similar replacement files in the universal patch, so maybe that fixes the issue too (whatever that issue is).

I believe this is the file you are looking for:
https://web.archive.org/web/19980421100047/http://ftp.microprose.com/ftp/mps-online/new-versions/ufofix.zip

I am also curious what the "Y-axis bug" is that this is supposed to fix. I've seen many online posts referring to it, but none of them seem to actually describe what the bug is.

After some Googling, this is my understanding:

The symptom of the "Y-axis bug" is that when you invade an alien base, the screen goes black with an error message saying "Couldn't fit y-axis". Hitting Enter a few times gets you past it, but a part of the alien base is blurred/corrupted.

The bug only affects the original v1 of UFO: Enemy Unknown. It's caused by a corrupted file which shipped with garbled content: UBASE_07.MAP. The ufofix.zip from above contains a bunch of MAP files, including a fixed UBASE_07.MAP. All the other MAP files are actually identical to what the game shipped with. ufofix.zip was released before any other patches or versions of the game.

Patch v1.2 for UFO: Enemy Unknown and later versions, as well as all versions of X-COM: UFO Defense, contain an updated UBASE_07.MAP that is newer than the one in ufofix.zip. As such, ufofix.zip is not necessary.

PS: UFO: Enemy Unknown is the original European release of the game, and these are the known versions: v1, v1.2, v1.2a, v1.3 and v1.4. X-COM: UFO Defense is the original US release of the game, and these are the known versions: v1.2, v1.4. The difference between the two is that UFO: Enemy Unknown also contains French and German texts, otherwise gameplay/bugs are the same in both v1.4.

Yep, pretty much what I thought, as OpenXcom has a similar universal patch and the MAP files are identical to those in the GOG version anyway (confirmed via MD5 hashes) but it has different RMP files (I stopped checking at that point).