Official FAQ confirms Flayer does not work with certain attacks, and it is intended
In other words, the fact certain weapons hardly get any benefit from Flayer isn't a bug but actually intended by the developers, assuming that statement is true for every instance Flayer isn't applied.
EDIT: No official information yet, but based on JP tests, the following attacks seem not to be affected by Flayer
- All Weapons: Focus Strike
- Gunlance: All Shelling
- Insect Glaive: Descending Slash
- Dual Blade: Blade Dance
- Switch Axe: Wild Swing
- Charge Blade: All Axe Attacks
- Heavy Bowgun: Wyvern Heart
- Bow: Dragon Piercer, etc.
Note this may require further testing to confirm those observations. Additionally, they don't address the inconsistency between different Flayer Levels, where it has been observed that Flayer 2 helps generating more wounds than Flayer 5.