In addition to my previous post, some files are being used in online(developed using CLIST and not CICS) also .
This could be the problem. If the file is still open in TSO, you would get the messages. If you have CLIST applications which are using these VSAM files, you should ensure the applications are complete and the VSAM files correctly closed before running the respective batch job.
When you next get the messages, look for that file being open due to application in TSO not complete. If application is complete, file may not have been closed correctly. Once you find what one is, it is probably the same for the others.