It definitely seems like a glitch. A lot of users on the Steam forums also have the same issue. There is a way to get rid of the B rank and that's to try and complete all "Run and Gun'" segments with a P ranking (Pacifist rank). Doing so will also unlock extra filter settings for the game (Black & White filter is the reward for all P ranks in Run and Gun).

To get a P rank, don't kill anything in the stage, complete it in under 2:00, and get 3/3 parry slaps. There's a special ability you can unlock later on in the game that makes your character invulnerable for a period of time. In Forest Follies, use the special ability to bypass the acorn machine and in Treetop Trouble, use it at the boss at the end of the level to bypass him and jump straight to the exit.

Just get a P ranking as that other guy said. I tried to get an A to no avail and just went for a P. In Treetop Trouble, equip the smoke dash, get 3 parry slaps from the Ladybugs, and then on the final Dragonfly mini boss that spits fireballs to shoot down the floating platforms you are on, jump over his head and dash to complete the level, you don't need to destroy it. That P ranking you get is higher than an A, even if it takes less effort.