Issues Saving/Overwriting Existing Files

We've seen instances where a user has been working on a project using an application such as Illustrator, and hitting the save button as they go along is creating multiple instances, as opposed to overwriting the existing file. Not sure if this is down to the system, application or SAN. The SANs are mounted via Samba 3.6.5 through a fileserver. The systems are Mac Pros running Yosemite and the applications are Adobe CC 2014.

I'm aware that the users have been deleting .ds_store files on occassion, could this potentially be related in that the metadata is no longer stored and therefore recognised by the system? Or am I barking up the wrong tree?

This doesn't occur all the time, but often.