Creator Backlash: While the Awdrys often cooperated with the show on early seasons, and even wrote some new novels for extra material, Rev Awdry was rather critical of its attempts at original stories due to their lack of realism towards railways, most infamously "Henry's Forest". Christopher Awdry also disliked some of his newer stories to contribute to the show, as well as being forced to make more Thomas-centric stories to tie in on it's main character.
To a lesser extent original director David Mitton, who was cynical about the CGI transition, but otherwise had faith in the series going on after his departure.
Hit story executive Sam Barlow admitted that the constant rhyming theme of the CGI seasons (especially Season 15) probably wasn't a great idea.
Executive Meddling: Negative examples — see Did Not Do The Research above. Also, Thomas and the Magic Railroad got butchered thanks to Hollywood executives being ignorami.
To elaborate, TATMR was not received well by test-screen audiences, stating that the plot and main villain were too dark, despite the film being complete at that point. The end result was a mess riddled with plot holes that resulted in HIT Entertainment taking control when the film failed. Later, when HIT was planning on bringing Thomas back to the television screens in America, they chose PBS, whose educational stance forced the show to be retooled extensively.
God Never Said That: One major rumor surrounding P.T. Boomer before his full role was discovered was that he was planning on destroying Shining Time Station and replace it with a highway. An interview with Doug Lennox, the actor who played Boomer, said that though such a plan sounded quite villainous, was never in any version of the script to begin with.
Keep Circulating the Tapes: The 1999 Fox Family series Storytime With Thomas. It would feature two episodes from series 1-5, sandwiched with an episode of Britt Allcroft's other show The Magic Adventures Of Mumfie in between. No VHS or DVDs were ever released of the show, and it was never sold to other networks.
Lost Episode: Though 'The Missing Coach' was never finished, the production team took a few still shots corresponding to this story. When these got out on the Internet, for a while some people did think the entire thing had been filmed.
Name's the Same: In the UK, Season 2 and Season 11 both had unrelated episodes titled "Dirty Work," but in the US, the former, taken from the Railway Series' Duck and The Diesel Engine, was re-titled "Diesel's Devious Deed." The US is not immune to this, however, as it had a Season 1 episode called "Thomas Saves the Day" (its British title was "Thomas and the Breakdown Train") and a Season 8 episode also called "Thomas Saves the Day."
The UK did this again with season 1 and season 11 where both episodes "Thomas in Trouble" (the US version of said season 1 episode is re-titled "Thomas Breaks the Rules". Also the season 4 and season 8 episodes name is entitled "Fish", which the name stays the same in all UK and US versions.
The Other Marty: Various voice actors in Thomas & the Magic Railroad were replaced during the post-production overhaul:
Thomas was initially voiced by John Bellis, a cab driver the crew met while shooting on the Isle of Man. He can be heard in one of the teasers.
The series' concurrent UK narrator, Michael Angelis, was the voice of Percy and James. Test audiences thought the characters sounded too old, and in the final version they're both Cross-Dressing Voices.
A few of the trailers feature Diesel 10's original voice actor, Keith Scott.
In Japan, the entire show was recast after the eighth season when the show switched stations.
The Pete Best: George Carlin joked about this after he replaced Ringo Starr.
Playing Against Type: George Carlin, the legendary comedian famous for his profane material played Mr. Conductor in the US version.
Recursive Adaptation: The show garnered it's own magazine series, with some of it's original stories actually adapted into episodes of the show itself in Seasons Three and Five. Incidentally the magazine's writer at the time eventually ended up lead writer for the show come Season Seventeen.
Recycled Script: Seasons thirteen through sixteen all followed an identical pattern: an engine is given an important job to do, but something else (usually an idea how else to do it, or simply not wanting to) keeps them from doing it. After making the same mistake three times, everything goes wrong, the engine learns the error of their ways and fixes everything Just in Time, says the moral of the story, followed by a Everybody Laughs Ending.
Ironically, this was also one of the reasons the original team stopped adapting stories from The Railway Series, feeling they had already adapted most of the unique stories their budget could handle.
Throw It In: Much of Neil Crone and Kevin Frank's voiceover work in Magic Railroad - particularly the banter between Splatter and Dodge. They were originally hired to improvise material for the trucks.
A few discarded stories from The Railway Series were planned for adaptation early on, but were canned due to time and budget constraints, or being considered too complex for children's stories (eg. "The Missing Coach" and "Gordon Goes Foreign"). A few other stories that were more loosely adapted are also the result of this (e.g. "Tender Engines", which was originally planned to be closer to the novel's "Tenders For Henry" until budget prevented them from making a full model for the Flying Scotsman).
The show was originally planned as a BBC kids show, but after only one episode (Thomas and Gordon, obviously), the show moved to ITV instead.
Several classic characters were originally planned to be part of the core Steam Team for the show's 2004 revamp, but a need for a prominent female character, coupled with problems on some of the models, resulted in the current cast of main characters.
Duck was one of the biggest considerations, and was actually going to be part of the Steam Team, but the need for a female character overruled this.