Question: What happened to the orphans at the end of Annie? Did they get adopted with Annie or are they still staying at the orphanage?
Answer: They are no longer at the orphanage since Miss Hannigan reformed and became a schoolteacher. So they are all adopted with Annie by "Daddy" Warbucks.
Answer: They're still staying at the orphanage, but it seems Mr. Warbucks is helping to fund them and Miss Hannigan has had a change of heart, so it's not so grim.
Answer: Annie and Molly both get adopted by Oliver Warbucks and become sisters ages 10 and 6 and live with the male family dog, Sandy and Oliver marries Grace Farrell and Grace becomes Annie and Molly's mom.
Answer: 10 year old Annie and six year old Molly and another orphan named Chloe get adopted by Oliver Warbucks and have the male family dog, Sandy and Oliver marries Grace Farrell and Grace becomes the girls' new mom.
Question: How did they make Kirk Douglas have a peg leg? How was he able to walk that way?
Answer: This movie predates the more advanced CGI that would be used these days. In older films, actors portraying an amputee would have their leg (or arm) bent back and strapped to their body. A prosthetic peg leg would be attacked to the lower appendage. The actors were also filmed from strategic vantage points so the bent part of the limb didn't show. When Douglas is seen driving a wagon, the seat was probably constructed so that his lower leg fit into a hidden compartment and the peg leg was attached on top to be visible. Douglas also wore rather baggy pants, and that would help conceal his bent leg.
Question: When Jen looks at the shard, he sees in image of a Skeksis striking the crystal, but why when the beings of light appear, do they say that they were the ones responsible for shattering it?
Answer: The skeksis and the beings of light are the same, each being a different side (good and bad) therefore it was there evil side (the skeksis) that struck the crystal.
Answer: He doesn't per se, the rats release him when they show up to move Mrs. Brisby's house.
Answer: Molly gets adopted by Warbucks and becomes Annie's sister and the other orphans get adopted by other families while a reformed Miss Hannigan becomes a schoolteacher.