Ok, I've been going through the quest book. This is not a full list of all quests with problems. But it is a start
Offering More Tier 6 can't craft Crystal Clusters, 3 quests give Crystal Clusters, no 4th Crystal Cluster atm.
Meka...Meka....Nism About half the mechanism items have no NEI recipies
Sanguinomancy Locked
Thuamcraft can make iron capped wand, doesn't satisfy quest
No way to make balanced shard
Even though iron capped wand doesn't satisfy quest, it still lets you make a worktable and thaumonomocon (right click wand on table and book case)
Haven't checked the rest of the thaumcraft quests
MFR no way to make laser precharge
Botania several quests allow you to complete them without doing anything
Second Chance can't get essence quest, water quest to complete
No way to make pink slime (no animals for slaughterhouse, may possibly be able to get animals from single use safari nets from fishing)
No way to make molten iron
Blood Tank quest no quest name, no reward
No way to make draconium items (may possibly get draconium ore in the end, one quest gives 10 ore)
No idea how to get dragon heart, kill dragon in the end?
Witchery, half the quests are literally unfinished
If you have any info on any of these quests please fill us in.