how to deal with falsely merged gene regions into one super-locus?

[Ruth-hals]

Hello, I used gffcompare to merge two gtf files with the following command: gffcompare -i gtffiles.txt

However, it seems that there are a falsely merged gene regions that are in fact two different genes. Do you have suggestions to deal with this? Is there a way to specify to only merge after they share at least 2 exons or at least X amount of overlapping base pairs?

I would be gratefull for your reply, Kind regards, Ruth