If both Mac OS and Windows use the x86 instruction set, why do we have to recompile for each platform?

If both Mac OS and Windows, running on Intel processors, use the x86 instruction set, why can't a program written using only C++11 (no OS Specific libraries, frameworks or API's), run on both without having to recompile for that platform ?

Ultimately the program gets compiled to machine code, so if the instruction set is the same, whats the difference ? What's really going on ?