You probably have better ideas than me to fix this
...but I think either
A) it goes away after time
B) can go away after i start using the GUI / goes away when i click on it
C) is in a different location when resolution is small

Same error here :( waiting for fix

Mismo error aqui. Esperando una solución

I have this same exact issue on my Macbook Pro. Fullscreen makes the UI overlap.

I found the solution to this issue!

 
Go to options,

Video settings,

And click on " GUI Scale "

Choose Large instead of Auto, mine was on auto and it screwed up the tooltip.

Using Optifine with GUI Scale "x5" is also an option and GUI is nearly same big as with vanilla "auto" option!