There is one actual VM (datastore2) but it appears to be two in the datastore (datastore1)

[djkwon]

We are currently operating datasotore with 4 units. A particular VM is actually in datastore 2, but it appears to exist in datastore 1.
The file is not visible in the actual datastore1.
When I edited the VM, the CD/DVD mounts the ISO of datastore 1, so I first removed the ISO from the VM, but I still see the VM in datastore1. What is wrong with this phenomenon??
Version is V6.7.

[degvm]

Try to switch the CD-Rom to "Client Device", not just disconnect the ISO. Also double-check a potential floppy drive connected to the VM.

[djkwon]

Yes, I switched the CD-ROM to Client-Device and the disk is not using datastore1's.
If you switch to Client-Device, it's normal not to be seen in datastore 1, but it's still visible.

[degvm]

have a look on the Settings of the VM: VM Options/ General Options, "VM Working Location" ? Perhaps that is pointing to the datastore1 storing the NVRAM-Files on that first Datastore. Also try a storage vMotion to the datastore2, which might dissolve that behavior.