I add variations to listings quite frequently, and occasionally experience technical glitches, but usually if I go back through all the stages one by one, it resolves, if not, I just close it off and re-open the listing and start the edits again - I don't use templates at all, though, so can't advise on that.

The process I use is open the listing editor, click "add / edit variations", and add what I need to there, I'll then click 'next', at which point a warning will pop up telling me my images etc will be removed, but continuing is the only way to save the changes.

Creating a new variation doesn't add it to the listing automatically, even though you can upload photos for the new ones, so on the page where you're able to add an SKU, pick your new variations from the dropdown menu (under the current variations, where there are blank fields), then click 'Add'. 

Proceed through all the other stages, and usually all goes well.

I hope that might help.