Dont blame version 4.1 - you will see that in all versions - even the latest ones.
To avoid this kind of problems here are a few things ...
- make sure you always cleanly unmount and detach volumes if you no longer need them
- make sure you always fix dead LUNs immediatly
- make sure only skilled persons are allowed to change / add / remove datastores
- make sure that your VMs that are backed up by tools like Veeam have a healthy VSS implementation
- make sure that your backup-tools are monitored carefully to avoid that snapshot chains build up and go amok
- make sure that /etc/vmware/esx.conf does not reference non-existant storage
also dont use very small and cheap USB-sticks as boot media for ESXi
It is also a good idea to practice a few procedures like rebuilding a partitiontable or extracting files when the VMFS becomes unreadable - as not always a reboot will fix the issues.