Assembly by stringtie
This seems to be a common problem. As @llrs pointed out, Ensembl, UCSC(genome browser and associated data) and NCBI records are not directly interchangeable. The ambiguity refers to annotation as well as the reference genome. The reference genome is identical, except for the chromosome naming convention, meaning a reference from Ensembl might not contain CHR prefix, whereas it will be present in one downloaded from UCSC.

To prevent such conflicts in downstream tools, it is good to stick to the reference and annotation from the same repository throughout the analysis and map the genes to gene names or whatever towards the end of the investigation. 

You can download all the associated data for T. aestivum which I beleive is the organism you want to study from Ensembl plants FTP download.