The ones I know off the top of my head
B3\B6: Bensonhurts Harway Avenue vs. B82 SBS: Bensonhurts Bay 38th Street
B36 Coney Island W 37th St vs B74 Sea Gate W 37th St (even though they never use it)
I also hate how they abbrivate Rockaway Parkway Station on the B6, B60, B17, B42, and B82 all differently. Consistency, dammit