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In your top level module, it looks to me like where you instantiate the module "up_counter", you have listed the ports in the wrong order. Same for the "hexadecimalcounter" instantiation.
You are using the "ordered list" method of module instantiation. At the cost of some extra typing, you could instead use the "connect by name" method and be less likely to have problems of this sort.
I think you may have some additional issues with your instantiation of "hexadecimalcounter". I am not clear on just what you are trying to achieve but the sizes of the signals you are connecting to the module are not the same as defined by the module. It also looks like your counter will count from 0 to 255 but the display will only go from 0 to 15.
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I am trying to achieve a hexadecimal counter which will count from 00 to FF. any additional comments or points to join in my code. What could be done to make it run ?