Good point Allicloud. Littlefoot does have a bit of a different color scheme for night scenes. I mean yeah, you can see a picture of what I'm talking about in my profile picture for reference, but yeah, it's just so... weird. XD And yes, I doubt his brown and cream would really become those turquoise hues in the darkness, as you said.
Which brings us to DarkHououmon's speculation of moonlight. I was thinking that was one possibility myself, and the moon DOES seem to look rather blue in that scene when Pterano looks up at it, but at the same time, Rinkus doesn't really change much in coloration. His light pink basically becomes dark pink, but Sierra becomes dark blue, and Pterano becomes light green and light blue.
His crest remains pretty much the same, with only a minor color shift. So it's really hard to say for certain if the moon is having an effect or not. I think it's still possible, but difficult to prove I guess.
I also wonder if the studio had a high turnover rate of animators like many studios do. Often times, a different team is called in to work on different movies, such as at Pixar. Pixar will have about a third of their animators that are the "core group" and never go anywhere, working on every project that comes up, but the other two thirds are cycled through every so many movies, as they want people with different talents for the different types of movies. If the animators were pretty set for a number of the Land Before Time sequels, then they'd be easier to track down and possibly ask (provided they have contact info of some sort XD I've actually done this before, and most animators are more than willing to talk about their work). An easy way to find out would be watch the credits I suppose.