Beside specific stories, there are two things in the general set up of Thomas that makes it IMO a toxic show.
- The trains, who have children's minds, are unquestionably servile. They obey a pompous and capricious elite (humans) and the narrator goes along for the ride. Obeying is very important for Thomas (who's physically constrained to spend his life on rails). He'll do whatever is needed to stay in his master's good graces. It is the perfect show to condition child slaves into compliance.
- The trains are racist, and it is normal and acceptable. Steam and Diesel engines loath one another. The show is presented from the steam team point of view, without an ounce of distance. The Diesels have inherent character flaws because of their engines. I just found a recent episode [1] where they kind of address that, but it is AFAICT a recent development.