When Tippy's mother states that she'll bring Spike back from his first visit to the Spiketail herd "before the Great Circle leaves the sky", the weather is overcast, and the sun not visible through the clouds. The next scene, however, shows a relatively sunny day. This could likely be within the same day.
The night of the big snowstorm, Ducky is seen sleeping with four other siblings. In the earlier scene when Tippy's mom and Ducky and Spike's mother interact for the first time, Ducky is seen with only three siblings. The latter is also true the morning after the snowstorm.
Music error: When Topps is calling for Cera, just like the other parents, who are calling their children that had disappeared, the music builds up, but then the track is cut off abruptly, and is replaced by the opening of The Rescue/Discovery of the Great Valley.
Like many dinosaur pop culture depictions, most of these dinosaurs depicted existed in different millions of years time (throughout different eras) and not altogether.
Ducky and Spike's mother tells Tippy's mother that there were no other spiketails in the Great Valley when she took Spike in as her own, but other stegosaurs have been seen in the Great Valley in the past sequels; some even having a few minor speaking roles. She might have meant, however, that there were none at the time, but some arrived later on.
Early on in the film, when Ducky begins to ignore Spike, and when Spike falls through the deep ice near the end of the film, Ducky incorrectly states that he cannot swim. Sure enough, after calling for their mother, he quickly sinks. Spike can be seen swimming throughout most of the series, even after this sequel was released, and is in fact shown to be just as good at swimming as Ducky.