Are they made of the same material, have the same size and type of tyre, same level of component wear, same tyre pressures, same saddle, same pedals, same bar tape etc etc etc?
If they aren't identical in every way, of course they can feel different (your thread title says they are different)
Even if not the same colour as obviously black bikes are much slower and red are the quickest
How are you defining 'feel different'?