Troubled Production: Mostly as a result of taking too much without seeing. The movie originally wasn't supposed to be a movie, just a higher budget 45-minute episode (instead of the usual 30 minutes), but the staff had too much trouble keeping it that short and eventually decided to turn it into a full fledged movie, with much of the staff in hindsight realizing that was too big a leap for much of them to handle. The project soon turned into a mess of too many new hires with misplaced management, constant budget overruns, long working hours, and the end result was a numerous amount of layoffs. For more info, much of the story was covered in this series of blog posts by Phil Fischer himself.
Other candidates to play Jonah were Bob, Larry, Junior, and Billy Gourd, but neither of them were uptight enough to fit the role.
The whale was originally designed to look more intimidating, but concerns that it would terrify kids lead to it being redrawn. Among the other designs were ones based on humpback whales, trout, and one that looked uncannily like Archibald, monocle and all.