Does a firmware (flash memory) in atmel mcus change on runtime (to store variables for example)?
Yes i do have a bootloader. and the corruption happens on the first lines mainly (1st to 8th line of the flash)

If your micro-controller has a bootloader then that means it has the ability to program it's own flash under software control. Furthermore it has code in the program memory that was designed to write the flash.
If you allow a processor to run below it's designed supply voltage, then you risk erratic operation. Said erratic operation could lead to inadvertant triggering of the programming code in the bootloader.