That could also go for SA, if you have level 3-5 you get medium thread and if you are 6+ you get advanced instead.

And for survival if you have the ninja at 5 stars already they would be removed from the pool of what you can get. I for for example, have over 100 frags for both Suigetsu and Yamato that are already 5 stars.
I never got any frags from them other then survival and elite instances rewards for first completion, and survival keeps giving me them over and over. How about different ninjas like the Sound 4, Asuma even Guy. If you have a ninja 5 stars if should be removed from your pool of ninjas

Here is a list of what each fragment gives as points for that system:
http://forum.naruto.oasgames.com/en/forum.php?mod=viewthread&tid=7548&highlight=fragments

In my case, if i refined all the extra fragments i would get this
Yamato- 109*2 = 218
Suigetsu- 106*5 = 530
MC- 54*5 = 270

all added up in a total of 1018 points, give or take if the list has some errors

I could exchange those frags for 100k coins, 1.5k cultivation runes, or a mix of both. Or 1/3 of the way to 10 Iruka frags.

NOT WORTHY, i would much rather have a ninja i dont even use to get 4 or even 5 stars then keep getting this extra frags, because stars will matter in the future for the new recruit system other versions have later on (if our version lives to that) while this extra frags are just sitting there. The last scroll you can get will need you to have 240 stars which at 3 stars ninjas would give 80 of them.

SO yes, i still think they should be removed from the pool once you get them to 5 stars.

BUT that is just a suggestion.