Hi!
As far as i know there is no way to see what is locking up your files.
We had a simillar issue. Our solutions was to restart every host in our cluster once at a time. After the 7 host out of 9 we were able to delete the files...
This can be done without down time... Try it out.
Use vmware-cmd tool from service console
for example
vmware-cmd /vmfs/volumes/......../vmname/vmname.vmx getstate - current state of your virtual machine
vmware-cmd /vmfs/volumes/......../vmname/vmname.vmx stop(reset) - stop or reset vm
than try to remove files.