Cheep Cheeps Are Not Harmless Part 1
In Super Mario Bros. Wonder a little detail was added for the Red Cheep Cheeps, that detail is that they bite Mario. This explains why Mario takes damage when he touches them similar to Goombas and Koopas.
We've known for a long time that Red Cheep Cheeps become Boss Bass or Cheep Chomp try to eat Mario, and one type of Cheep Cheep bites Mario in Super Mario Sunshine.
But we hardly see how Red ones harm Mario, especially since they typically never actively target Mario like say Spiny Cheep Cheeps do. The only indication we had that they do this was from The Super Mario Bros. Movie, which only parallels this behavior.
We know they do this because they are minion's of Bowser, and are shown to be just as intelligent as any other creature in the Mario world.
This is also why hypotheses that place Mario as evil and Cheep cheeps as harmless are just wrong. Written by Eris the Lorekeeper Part 2 is in the works