I have attached the file, any help would be great.

Here's the first line in the file:

--
Mito intergenic_50 exon 1 680 . + . gene_id "INT50_3749" ; transcript_name "INT50_3749"; transcript_id "INT50_3749"; gene_name "INT50_3749" ; Note "intergenic regions 50 nt from a coding sequence"
--

As it turns out, the file is not technically a GTF file. The GTF spec is here:

http://genome.ucsc.edu/FAQ/FAQformat#format4

and the requirement broken by this file is:

--
The attribute list must begin with the two mandatory attributes:

• gene_id value - A globally unique identifier for the genomic source of the sequence.
• transcript_id value - A globally unique identifier for the predicted transcript. 
--

Where did you get this file? If there are prominent tools that are producing almost-but-not-quite-compliant GTF files, it may be necessary for Galaxy to relax its requirements a bit.

Thanks,
J.