This message started appearing because during my development stage my Project Manager created some views for entities directly on the production. So the 2 CRM systems went out of sync. We both tried alot of things to solve it, but all in vain. I also contacted Microsoft CRM help team(Customer Source), they suggested using CRM tracing tool.
Finally, we used the tracing tool to monitor the uploading process on production system. We found out problems with a view. I removed that view production system and tried again. Again and again I removed many view from production system. Then only after removing all the views that were created after I copied the CRM system from production to staging, I was able to upload the customizations to Production system.