Overlapping repeats in output? 1.5Mbp gap in gff?

[nikostr]

Hi! I was under the impression that EarlGrey filters out overlapping repeats. In my gff I have some examples similar to this:

ptg000135l      Earl_Grey       LTR/Gypsy       1       41928   257454  +       .       TSTART=1;TEND=55496;ID=RND-4_FAMILY-103;SHORTTE=F;TEGROUP=CTG_135|RND-4_FAMILY-103|1;KIMURA80=nan
ptg000135l      Earl_Grey       Simple_repeat   7441    7471    31      +       .       TSTART=1;TEND=30;ID=(AT)N;SHORTTE=F

Is this expected?

Looking at distances between repeats, I find that the vast majority are located adjacent to each other, but I have a single region on the tail end of one of my bigger scaffolds that has a gap of 1.5Mbp, with a small number of repeats present right at the end of the scaffold. If I wanted to understand what's going on there, do you have any recommendations on where to start?