The whole film is Professor Bomba telling somebody the story.This would account for the somewhat disjointed storytelling, seeing as Bomba himself is more than a bit scatterbrained.
Professor Bomba is slightly faster than ordinary humans.When we see him from a non-Leafman perspective, he often seems to be moving and reacting and talking too fast. Also, this would explain how he discovered the Leafmen. If his speed differential is less than normal, he'd be a bit more able to see them naturally.
The forest is still doomed.We're told that the Queen Tara held the forces of decay at bay for the sake of balance. Now that the forces of decay have no heir, the balance is upset. Very likely all that new growth will suck up all the nutrients from the soil. Nutrients that would've been produced by the forces of decay. While not an immediate problem, it will eventually become an issue.
Mandrake wanted to use the pod to bring his son back to life.It is explicitly stated in the film that the pod will always choose a queen to rule the forest; however, Mandrake seemed to think that it would provide a male heir. This is because he assumed the pod would choose his son as a vessel for the forest's power. The fact that Dagda was dead wouldn't be a problem — as Mandrake says, if the pod blooms in darkness, it belongs to the boggans, and their domain is rot and death.
Ronin and Nod's father killed Mandrake's family.Mandrake mentions that Dagda took after his mother, but we never see her or hear about her again. Boggans are apparently born as larva, but bugs tend to breed by the dozens. Ronin and Nod's father infiltrated the boggan base specifically to take out the royal family. They managed to kill the mother and nearly all of the eggs, before Nod's father was killed and Ronin was driven away. That's why Mandrake hates Ronin so much — he's more than just head of the leafmen, he's the man who killed his family.