i noticed this in particular with the Con+1 that adds Con Save proficiency.
it simply doesn't do anything sometimes.
i cant figure out what causes it to not apply thought, as when i selected it on all 4 character slots 3 of them got it but one didnt.
so i reloaded before the level up and tried again the same exact way and this time it didnt apply to any of them.
I've run into issues with feats. The Sylvan Archer feat, or whatever it's called, reliably gives me +1 DEX but never mitigates the cover AC bonus that enemies receive. Other people have reported issues with that feat as well. So you're not alone in having issues with the feats at present.
The feat that applies half damage if an enemy saves against a cantrip attack doesn't work. At least not with sacred flame.
The +1 Con and an extra HP per level feat would not apply on my fighter. I don't know if that feat is just not implemented or if something is wacky with feats in general.
Update: Err, I got my +1 CON and hitpoints (unhealed) after I left the camp and walked around a bit.
Took Creed of Arun (+1 Con, Con Save Proficiency) on my cleric. Feat didn't seem to take effect until I quit and reloaded game (at which point I had the save proficiency and my Con went up to 16) but I still didn't get the associated increase in HP from having the higher Constitution.