When Jerry finally decides to go play with Lassie, we can hear someone off-screen give Lassie a command. Right after Jerry says,"Let's have fun now," and hugs Lassie, a man's voice clearly speaks a word off-camera, and Lassie looks in that direction before running off with the boy.
If you watch Claude Jarmin Jr.'s lips closely, you will see that he is using the working title of the film, "Sun in the Morning". Jarmin had to redub the line when the film was released as "The Sun Comes Up".
When Jerry is lighting the oil lamp for Helen, he speaks a line that includes the movie title, but the voice changes to a different-sounding voice while the line is being spoken and the words don't match the movement of Jerry's mouth.
When Helen first arrives at the cabin, she spots some birds in a nearby tree. These are Stellar's Jays, which in the US are only found in western states like California. However, the film is set somewhere in the east, near Atlanta, where these particular birds are never seen.