I frequently get a message when I'm saving a file in Twisted Wave:

This document's file has been changed by another application since you opened or saved it.
The changes made by the other application will be lost if you save.  Save anyway?
Save    Don't Save

I get this message when I save a file I'm working on, then save it again after making more changes.

I get this message too, but only if I've applied some type of processing, like amplify or normalize or something (I forget specifically).

I think it is a bug?

It has to be because otherwise you wouldn't be able to do this processing on the file then continue editing.

I could reproduce the problem, indeed. Thanks for reporting it. In fact, it happens only with the 64-bit version of TwistedWave. I could fix it, and the correction will be available in the next update. Until then, you can use the current development version:

http://twistedwave.com/download/TwistedWave64-1.8.0.13.dmg

There was a small bug. Use this one instead:

http://twistedwave.com/download/TwistedWave64-1.8.0.14.dmg

Sorry :)