That menu graphic is an uncompressed image and just so happens to be mostly represented by the hexadecimal value 0xFF (which is indicative of free space in a FR ROM). Thus, if you're not watching out where you're inserting something, it can easily overwrite that graphic.
To fix it, you have two options. Firstly, you can copy over the graphic's data from a clean ROM and restore what's been over written. To do this, C+P the data ranging from 0x4566E8 to 0x4568E8. This will fix the window, but it will have the side effect of breaking whatever it was you inserted there to corrupt the graphic in the first place. You will have to reinsert that somewhere else aswell, which is easy to do if its something simple like a script.
As a second option, you can remove the graphic entirely by writing 00 00 00 00 to 0x55910,
thanks to deokishisu.
When hacking FireRed, remember to always insert things above the offset 0x720000 as that is where almost all of the safe space in the ROM is. Good luck!