How can I check the changes for the fields at form alter submit? I am using hook_form_alter() with custom submit handler (). 
At submit I want to check if there is any change in the content except node->expire then my custom code will run. 

but at $form_state['value'] I am also getting: nid, vid, uid, created changed etc. 
and I have field type as taxonomy term reference and media files. 

I do not want to  hard-code the fields name as admin may add new fields later on.
Try comparing both $form_state[input] and $form_state['values'] .

After that check both values using the key's in foreach loop and compare both values, if changed then do your things there.