I could be wrong about this, but the problem could be that street fighter did not make a difference as to which slot the coin was placed in, you could put your coin in slot one or two, and it could be used for either player, and TMNT cabinet was deticated coin slots and players (if you put the coin in slot one, you could only be player one - Leo and you could only play leo on joystick one; and then slot 2 =player 2 which is mike on joystick 2...same for coin slot three and four respectively)
your cabinet may just have wired both coin slots as just one switch...but thats just my guess. I think it should be not toohard of a fix.