From an HTTP perspective, repeating query parameters isn't illegal, so BIG-IP doesn't disallow it as a proxy.
From a Web App perspective, the behavior when handling multiple repeated query parameters isn't defined in any explicit way.
If this repeating-parameter behavior is breaking stuff and is caused by the app itself, you'll need to report the defect to the web app vendor.
If this repeating-parameter behavior is breaking stuff and is caused by middleware (BIG-IP, irules, or whatever), you'll have to figure out exactly where it's happening and use some kind of workaround.