Wikipedia editors should be able to enter whatever value in citation template "url" (or aliases, see T301516) parameters, including invalid URLs (i.e., badly formatted). I assume Citoid would respond with a 400 Bad Request error in these cases, or it may try to resolve it somehow else without using Zotero translators (e.g., as a free text query). This would unnecessarily load the Citoid service (see T301510), and may even give us incorrect results (e.g., if the query is interpreted as free text).
To prevent this, consider using a library to validate that the value found in the "url" parameter (or one of its aliases) is a valid URL. Consider doing this at an early stage, such that a citation template can be dropped if it does not have a valid URL (just as we currently drop citation templates without URLs)
On the other hand, apparently some of our calls to Citoid are returning 404 errors. The most likely reason is that the resource no longer exists. However, I tried a request for "http://repositorio.unb.br/bitstream/10482/5542/1/2008_NeideMOGodinho.pdf" and got a 404 error, even though the resource does exist. Zotero does not support translating PDFs. See T136722 and T214038. I haven't checked Citoid's source code for this, but I wonder if we are getting a 404 response because of that.
We should avoid making Citoid requests for URLs pointing to PDF files. As far as I know, the only way to know for sure if a URL is pointing to a PDF file is checking for its "Content-Type" response header. We could make a separate HEAD request for all URLs before calling Citoid, but that would mean an extra burden. Alternatively, as a partial workaround, we could drop all URLs ending in ".pdf" at URL validation, assuming that they are in fact pointing to a URL file.