It seems to be an problem with WAB Version 2.1 when using in IE9 having widgets(for eg. SmartEditor) which are doing applyEdits.
WAB 2.1 is passing a parameter “wab_dv=2.1″ to every request, so in case where applyedits are being done the request url becomes invalid due to this parameter and the operation fails.
Following is the sample request which is generated when we do applyedits (as it is post operation proxy is applied):http://<server address>/proxy/proxy.ashx?http://<server address>/arcgis/rest/services/<ServiceName>/FeatureServer/0/applyEdits&wab_dv=2.1
The appending of the WAB version happens in the env.js and it is done to avoid cached data. If this is causing you and issue then you can comment out the portion of the appendDeployVersion function that adds that to the url.