Is there either a fix or a workaround for this?
The best I can tell from that error is that Neocities is responding with junk information instead of telling the gallery maker whats wrong ~ it does this a lot, and its really been painfully unreliable to work with

The only work around is to try again at another time, maybe NC will sort itself out; otherwise you can use the NC
CLI to manually upload your gallery (I tend to do this with mine).
(Assuming you want your gallery to be MYURL/gallery - put your output gallery in an empty folder, then run to CLI from that folder and use the push command!)

manually organize the folders in the gallery
Numbering is your best option! The Gallery maker has no UI for sorting or organising; it just replicates and formats folders and files; its not within its scope to add UI to do that. However I presume the issue for you here is that you just want the links on the index page sorted?
You can always edit the index file yourself after it generates, or just create your own and link to it, instead of the default index; alternatively you could even include a javascript that sorts the links based on your own parameters!