Well, in LBT 8, Ducky's mother comments that there were no other spiketails in the Valley when Spike arrives, to which Tippy's mother replies, 'until now.' Though in the previous films, LOADS of background characters who were spiketails could be seen...in the second film, one even seemed to be an almost fatherly figure to Spike...
In the same film, when Mr Clubtail is complaining about the snow, he seems to have had a minor operation...

: suffice to say, he is now Mrs Clubtail. I know it was most likely meant to be a different character, but I remember it shocking me to the core when I first saw it.
In the fifth one, the land path that connected the island to the mainland was seen growing back a couple of times when shots of the sea were shown.
But literally the best continuity error (some sort of error anyway) has to be on the TV episode, The Great Log-running Game. Cera was heading towards a waterfall and all the two-legged characters were pursuing her on logs. Littlefoot and Spike were attempting to help Mr Threehorn block the path of the waterfall, but in one shot, Spike was replaced by Cera... :huh: