When being teleported up by a fast clock the players velocity consistently builds up on the split second in between where the players falling which can allow a player to die from fall damage falling from two blocks above the ground.
To test:
1. Make a new world (this device can get annoying and you probably won't want this in a world you use often)
2. Make the contraption in the picture (comparator clock with empty command block)
3. Put the command tp @p ~ ~2 ~ in the command block
4. When in survival mode turn the clock on and try jumping.
You can also witness this phenomenon when jumping from a height that would normally be fatal, but you use a teleport clock to teleport yourself slightly up so you fall gently to the ground. Except you won't fall gently because your velocity will still accumulate during the falling time.
I would suggest (as someone not familiar with professional programming) that the velocity be reset every time the player moves upward.

Also, you probably noticed there is a strange visual glitch when teleporting as well. Not sure if that is a separate issue or what...