I go to my enterprise wiki site collection Master page gallery, and the upload page can be load correctly.
The upload page (_layouts/Upload.aspx) is used for all library for uploading file, please check if the upload page is working well in other libraries (even in other site collection or a new wiki site collection).
Also check if this issue happens in IE9/10, Firefox, Chrome, etc. see if it is related to one particular browser settings.
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