Check to make sure that the item you're trying to remove a stat from actually has a stat to remove. Also, if you haven't separated a single stone from a stack, then do so. The Transmuter won't let you extract a stat with more than one extraction stone in the extraction slot. Also, don't forget to hit the confirm button.
If that doesn't help, try restarting the client. I've had mine sometimes refuse to transmute items after I've been online for a while, and a relog usually fixes the issue.
I have single stacks of the random attribute extractors but my gear has 6 stats. Maybe I've misinterpreted what stat can or cannot be extracted. The 6 stats I have are dext/patt crim/hero/glor and stam/patt crim/hero/glor. Are those stats that can't be removed? 'o.0
I've also restarted the client and I've been trying multiple days on using the random attribute extractors, no luck. Chances are, it's probably just my gear that cannot have a random attribute extractor be used on since I've only tested it on a crossbow I've had.