Questions/Observations.
1) When the animals need help, they call CODY to help. It would make more sense to call an adult.
2) CODY manages to climb a cliff that's at least 100 feet! Without any equipment!
3) MCLEACH is wanted by the authorities. They have his name and photo, so why can't they find him? It's not like his truck is small and silent.
4) Why are MARAHUTE and JOANNA the only animals in the movie who don't talk?
5) If MCLEACH doesn't know where MARAHUTE is, how did she get trapped?
6) It's impossible that there's always a mouse to witness a crime and call the R.A.S.
7) THE CHAIRMOUSE says they must find BERNARD & BIANCA at once. Why? Isn't the point of reuniting 1 mouse of each country that he can choose? Just because those 2 are the best it doesn't mean they have to do every mission. Actually, by trying to reach them, the R.A.S. wastes time that could cost CODY's life.
8) Were BERNARD & BIANCA dating from before the movie started? It's never clarified.
9) BERNARD misunderstands BIANCA, and he thinks she does want to marry him inmediately. Even though they go to the headquarters, he doesn't realize about his mistake until she tells the CHAIRMOUSE that they accept the mission.
10) In order to land, WILBUR communicates with the Australian base via radio. How? I never saw him with any communcation device. If he had one, why did the mice had to use a sardines can as a seat?
11) After being released, how can CODY not hear MCLEACH's huge truck behind him?
12) How is CODY able to walk from MCLEACH's place to the nest after probably having spent hours without food and water?
13) Why does MCLEACH want to get rid of the eggs? Won't he get more money by having more eagles?
14) BERNARD somehow heard MCLEACH tell JOANNA to eat the eggs and, despite being tiny, hid the eggs and replaced them with rocks of the same size. In less than a minute.
15) Why didn't JAKE mind that BERNARD & BIANCA got engaged?
There are other loose ends where we can assume the answers, but I felt they should've been shown anyway for closure. I'm talking about these:
16) What happened to the animals that MCLEACH trapped?
17) Did CODY's mom found out he was alive?
18) Will CODY's mom snap out and realize she shouldn't let him go out of the house all day on his own?
19) Will the baby eagles think WILBUR is their mom instead of MARAHUTE?