Maker gene prediction error

Question

[the_cowa]

From the output GFF of maker output, I grepped the location of genes (CDs). When I am comparing the maker predicted transcripts (all.maker.transcripts.fasta) and sequences based on the locations some of the transcripts have different sequences. Is it normal or is there an error on the prediction? and how to remove these transcripts?

[Juke34]

Transcripts contain UTRs I guess