Proper clearance when printing parts that need to together is critical. All 3D printers print holes undersized and pegs over-sized. This fact can effect parts fitting together, but improper clearances can also prevent other objects from fitting into a print (ex: metal support rods in wind tunnel models). See printer specific section for clearance recommendations data by printer. Looking at Figure 1: Clearance, one can see how the 2 mating halves do not meet due to a clearance error.
Figure 1: Clearance