The problem must be somewhere else
In[154]:= states = Range[0, 5];
Count[states, 0 | 1 | 3]
Out[155]= 3
that's correct (Mathematica 10.1, Windows 7 64 Bit Home Premium), because 3 entries of {0,1,2,3,4,5} fullfill the pattern of being 0 or 1 or 3. Possibly the Alternatives sign | got the wrong key on problem owners key board?