We have experienced this problem before too and we have found it is associated with multi-variation listings.

If you change a variation (add or delete) on an active listing and when you are going thru the save and submit process if you forget to select the option to save back to your asscoiated Selling Manage Template you will get this fault some time down the track when you next go to revise the listing. The active listing will work fine and buyers can access the new variation no worries.

We found it to happen if you try to edit quantity available some time later on.

We have not been able to find any way to fix this once this misalignment between template and active listing occurs.

We have had to end the active listing, delete the template and go right back to the inventory item and start all over again.

Add back the new variation to the inventory item and create a new template against this and then go on the relist the item all from scratch.

Then the problem is solved. But you have lost all your sales history by doing this.

You need to be careful when editing variations on active listings as the default when you submit the edits is to submit the active listing ONLY. The default should be to save to the template as well. So if you forget to do this you have just created yourself a problem you won't even know about until some time down the track when you next try to revise the listing.