Wake up kicks have invincibility that's it. Some moves have hurt boxes than sit a good distance behind their hit boxes, meaning they can hit you but you can't hit them most of the time. These moves are not invincible, they are just hard to hit them out of.
Jann Lee's 66K or 3K are good examples of this. To hit him out of either of these attacks you have to connect an attack to somewhere on his upper leg, but he only has to hit you will the end of his foot. This results in him winning 99% of the time.
The red box is the hit box (the bit that hits the opponent) and the yellow box is the hurt box (where she can be hit). But sometimes the yellow box is hidden way behind the red box meaning hitting them out of the attack is near impossible.
If a move is invincible like a dragon punch, the entire yellow box disappears meaning it is impossible to hit them out of the attack. I doubt this is the case in DOA5.
Edit: In regard to what hoduken said, some grabs have hold properties (OH/Catch Grabs) where at a certain point in their activation their can go through attacks and land the grab. This is only very specific grabs and does not work against air born opponents. I wouldn't class them as being invincible.