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URLs break when there is a space instead of an underscore. 
Example: 
http://www.website.com/09876/WikiProject Foo/
http://www.website.com/09876/WikiProject_Foo/

Would it be possible for the software to recognize a URl and if a space is present treat it as an underscore?

URLs are conceived as having no spaces, so spaces serve as delimiters. e.g. [http://www.website.com/09876/WikiProject Foo/] would render a link to http://www.website.com/09876/WikiProject with "Foo/" as shown text, whereas [http://www.website.com/09876/WikiProject_Foo/] would render a link to http://www.website.com/09876/WikiProject_Foo/ with "[1]" as shown text. Suggesting WONTFIX.

%20 should work in place of space.