Your assumption is correct! We've all been there.
...and let me guess, it was a very complex set of bends and was otherwise perfect...
...yes, that's the way it usually goes.
Based on you pictures, it looks like you got lucky and your "fix" was to simply re-terminate the ends. It appears that you used the normal tube cutoff tool which can't quite get up next to the flare due to the shoulder on the tool. To save a little bit of material, you can simply cut off the flare only using a dremel or hacksaw, then file the end square. Sometimes that little bit of material you save is the difference between scrapping the whole line or not.