I parked my car under a tree and needless to say there were many birds in the tree and it was a hot day. Anyway I cleared the droppings off and it looks like the droppings somehow have melted the paint or wax or something. Anyone else have this problem or know what it could be or what can be done. Will wax typically cover that up?

Happened to me. Bird drops (NYC pigeons) and berries.
Solution: compound. I have used 3M with good results. Any compound with do as long it doesnt have heavy/large particles in it to prevent damaging the clearcoat.

PS: dont 4 get to wax after youre done with the compound.

I wouldn't use anything too harsh. I recommend Meguiars ScratchX. It may take 3-4 tries, but it will eventually take out the bird etchings. You will need to put a good coat of wax afterwards.

Here is a thread on the Meguiars site, http://www.meguiarsonline.com/forums/showthread.php?s=&threadid=1516

depends on how deep they are. Is there still clear coat or did it go all the way to the base coat or lower. I bought a 2003 sentra specv new from a dealer and after washing the HORRIBLE wax job off that they had done realized that there were holes all the way through the base coat all over the entire car. Long story but yeah tree sap and bird droppings can do a lot more damage than people think.