List of characters who can cause wake up attacks to whiff (flip kick and ex flip kick have the same hit box):
Scorpion: sweep whiffs all
Liu kang: sweep whiffs all
Kung lao: sweep and D3 whiffs all
subzero: sweep whiffs all, D3 whiffs flip kick and ex shadow kick
sindel: nothing
ermac: D3 whiffs all
reptile: sweep and D3 whiffs all (sweep especially), D4 whiffs flip kick and ex shadow kick
kitana: sweep and D3 whiffs all, standing 3 whiffs nut punch
Johnny Cage: nothing
jade: D3 and sweep whiffs all (sweep especially)
mileena: D3 whiffs all, D4 whiffs flip kick ex shadow kick and nut punch
nightwolf: sweep whiffs flip kick and ex shadow kick
cyrax: sweep and D4 whiff all, D3 whiffs nut punch
noob: sweep whiffs nut punch, ex nut punch and flip kick, D3 whiffs flip kick and ex shadow kick
smoke: sweep whiffs flip kick, ex shadow kick and nut punch, D3 whiffs flip kick and ex shadow kick
sektor: sweep whiffs both nut punches
This list will probably never get completed, since there are so many attacks that alter spacing and hit box that can cause wake up attacks to whiff. A lot of attacks that can cause wake up attacks to whiff need good timing, making safe meaty pressure difficult.