Basic functions not being seen
This function commerce_cart_order_product_line_item_delete is in commerce_cart.module in line 1259 tnen in line 1268 call commerce_entity_reference_delete, function should be in commerce.module file line 124, check the function exist there.
This is some strange if the function exist in commerce.module and return fatal error,
I suggest first be sure that the function exist in code then  clear cache and then try again.
It is allowable call any function in any custom module and drupal not have restriction about this subject.