With Sharepoint, when we want to upload a file, the « Add as a new version to existing file » is checked by default, and that could be an issue for you.
Here is a JavaScript fix to add into your masterpage, just before the </head>
tag :
<script type="text/javascript"> function DefaultUploadOverwriteOff() { if (document.title.indexOf("Upload Document") > -1) { var input=document.querySelectorAll("input"); for (var i=input.length; i--;) { if (input[i].id.search(/\_OverwriteSingle$|\_OverwriteMultiple$/) > -1) input[i].checked=false } } } _spBodyOnLoadFunctionNames.push('DefaultUploadOverwriteOff'); </script> </head>