Executive Meddling: Mona Lisa was originally going to be a female turtle, but Eastman and Laird rejected it, so she was reimagined into some kind of lizard, which is why her head and feet look like the TMNT's. Supposedly they still didn't like her even after these changes, and ordered the makers of the show not to use her again.
According to that other wiki, Mona Lisa would've came back anyway, some time after the 8th season but the story scrapped in favor of the Lord Dregg and Carter story arc instead.
Network meddling was also responsible for Shredder and Krang being Put on a Bus and replaced by Dregg during the ninth season. They also forced the show's creators to introduce a "hip" new character, eventually resulting in Carter, who was pretty much an African-American Expy of Keno from the second TMNT movie. After these changes weren't liked by the fans, rather than admit they might have been slightly misguided in these demands, the executives fired head writer David Wise and replaced him with Jeffrey Scott, who had never even watched the series beforenote (and actually ended up persuading Wise to come back as an uncredited co-writer after being unable to get to grips with the characters), speeding TMNT '87 to its demise.
Fan Nickname: "Clonatello" or "Duplicatello" for Donatello's Evil Twin duplicate he creates in "Donatello's Duplicate".
Name's the Same: In season eight, there's a villain named Megavolt, who shares the same name as another villainous character named Megavolt.
There's also some Fridge Brilliance in that episode since Megavolt wanted to destroy the D.W.(Dark Water) company out of revenge. D.W. is also the nickname of Darkwing Duck.
Also Baxter Stockman's Mouser robots have the same name as King Koopa (Bowser)'s assistant in Super Mario Bros..
The Other Darrin: Several voice actors would occasionally have replacements during particular episodes:
Shredder was the biggest example, due to James Avery's other work; he was substituted by Dorian Harewood for a lot of the later Season 3 episodes, and then Jim Cummings on and off for the next few seasons. He finally bailed out the show for good after the first five episodes of Season 7; Townsend Coleman (the voice of Mikey and the Rat King) voiced Shredder for the rest of that season, and William E. Martin took over the role permanently in Seasons 8-10.
Raphael also had a few different voice actors over the course of the show; Thom Pinto voiced him for a few Season 3 episodes, Hal Rayle filled in for the "Vacation in Europe" episodes, and Michael Gough (no, not that one) replaced Rob Paulsen for the final season.
Donatello and Bebop, who were both usually voiced by Barry Gordon, were also replaced for part of Season 3 (seeing a pattern here?) by Greg Berg.
Vernon Fenwick was voiced by Pat Fraley in Season 1, but changed to being voiced by Peter Renaday in Season 2 to balance out the workload of the actors (Fraley did Vernon, Krang and Baxter Stockman in Season 1, while Renaday only did Splinter).
Leatherhead was originally voiced by Jim Cummings, but Peter Renaday voiced him for his final appearance in "Night of the Rogues".
Word of God (David Wise) has admitted April's yellow jumpsuit and minicamcorder outfit was based on Fujiko Mine's outfit from the Japanese anime Lupin the Third. Specifically, her outfit in The Castle of Cagliostro.
What Could Have Been/Missing Episode: There was originally going to be an episode called "Shredder in Love", but it never got past the script stage. Renae Jacobs even recorded lines for it. Little is known about the plot, but rumours state that the love potions from "Green with Jealousy" might have been reused.
Write Who You Know: Zach (the "fifth turtle") was allegedly based on one of the writer's kids.