Tracker/WMG

The whole Doomsday Device wasn't buried under the Watchfire-pieces of it were in different locations

 * This would explain why the fugitives had spread out so much by the end, though the weapon actually did appear complete when it was shown.

Mel's father didn't die in the boating accident mentioned in the show 'bible'-he faked his death

 * This theory came to my mind after the plot in Animorphs where the Yeerks faked the death of Marco's mom that way. The resoning could be nefarious, like a government group or other aliens wanting him captive, or he could have done it if someone was after him, hoping it'd get them to leave his daughter alone.