Character mistake: When Flynn opens the secret compartment in the Buddah, he pushes the signs for 'me' and 'e' to spell 'me'. But that is hardly how 'me' is spelled in that ancient language.
Character mistake: When Flynn is in the treetop in the jungle he says their position is minus X degrees latituded and minus Y degrees longitude. Positions are not indicated with minus - but North or South (of the Equator), and East or West (of Greenwich).
Character mistake: Flynn has been reading for a while, taking notes, spreading books around, etc. - when Nicole arrives and says that it was nice to watch take-off from the cockpit. The plane must have been in the air for a long time by then.