Technically they were completely different creatures. Razhar was a dog and Tokka was a turtle whereas Bebop was a warthog and Rocksteady was a rhino. Being based on a darker comic book and that rocksteady and beebop were cartoon/network creations that the original creaters weren't thrilled with. It came down to sticky rights issues. Eastman and Laird apparently created Rocksteady and Bebop so that Playmates would have more characters for the launch of the TMNT toy line. They were then used in the cartoon and Archie Comics. So using them would've meant New Line would have to pay some $ to other corporate entities, and it was cheaper to just create new stand-ins.

Even though they clearly weren't a rhino and warthog, kids I knew always just called the characters from the movie Bebop and Rocksteady anyway. We wanted them to be them, so I guess in our heads, we referred to them as the cartoon characters.