ok, the really easy to understand reason and fix for this
Hammer checks entities current keyvalues (the ones when 'smartedit' is off) against those in the loaded FGD.
If you've created a key that doesn't exist in the FGD, then it will flag it as having 'unused keyvalues'
Most common cause of this is by changing the entities angle with the compass, which adds in an 'angles' key to the entitiy with Z X Y coords.
To remove the problem from specific entities, open up the FGD and find an entity that already has an angles flag, copy it into the body of the problem entity and hammer will now shutup spamming that damn error.
If the entity doesn't need any form of starting angle information or some such, just uncheck smartedit, select the angles key and press delete, and stay away from that damned compass!
Never ever ever try to 'fix' the problem (using 'check for problems') as you'll find hammer tends to mess up everything.
Way back when NS used to be good, the original FGD was a mess, NO entities has proper angles flags in them and a lot of keys were undefined, which propogated this problem a lot. Took me ages but I edited every single entity in the FGD to remove the problem, thinking NS mappers would love me for the time and annoyance saved; and then I was banned from their forums and noone actually downloaded my fix. Lovely.