Have you REALLY assigned inputs and outputs of your top level to your FPGA pins ?
Could you post the interesting parts of Quartus compilation reports ?
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but all named pins (2-input & 1-output) are assigned manually by me.
the other 744 assignable pins were assigned randomly and that affects my output. How do i solve this pls?
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Are you sure about the pins you assign ?
I don't understand what you want to mean with the second sentence because it is trivial : if you assign correctly your useful pins, you don't mind about the others (of course if there isn't any conflict)
You can set unused pins as "input tri-stated" or "output driving ground" (be careful about conflicts) in Quartus menu > ....