This question has been asked and answered on SeqAnswers: Default cufflinks, Warning: Skipping large bundle. You can also refer to the Cufflinks Manual. See the --max-bundle-length option which states that it determines:
Maximum genomic length allowed for a given bundle. The default is 3,500,000 bp.
A 'bundle' is the size of a genomic region that is expected to contain a single gene that is being observed by a read group assembled by Cufflinks.