First of all, no you didn't.
Those 3 quests are ONE TIME ONLY and therefore you have missed a TOTAL of 9 seal frag.

Secondly... it took you a week? really?
While I do consider this a "bug", the fact that it is very easy to cir*vent makes it a rather unimportant one. I can't say I feel particular sorry for people who are affected by it.
To be clear, I ain't blaming you, because it IS a bug, but I also don't feel sorry for you.