Duplicate exons, overlapping CDSs in output

[nikostr]

One piece of my output looks as follows:

ptg000006l	LiftOn	gene	86505371	86507566	.	-	.	ID=g31624;source=Liftoff
ptg000006l	LiftOn	transcript	86505371	86507566	.	-	.	ID=g31624.t1;Parent=g31624;mutation=frameshift,stop_codon_gain;protein_identity=0.718;dna_identity=0.652;status=LiftOn_chaining_algorithm
ptg000006l	LiftOn	exon	86505371	86505373	.	-	.	ID=exon_138261;Parent=g31624.t1
ptg000006l	LiftOn	exon	86505371	86505373	.	-	.	ID=exon_138261;Parent=g31624.t1
ptg000006l	LiftOn	exon	86506533	86507566	.	-	.	ID=exon_138262;Parent=g31624.t1
ptg000006l	LiftOn	exon	86506650	86507566	.	-	.	ID=exon_138263;Parent=g31624.t1
ptg000006l	LiftOn	CDS	86507413	86507566	1636	-	1	Parent=g31624.t1
ptg000006l	LiftOn	CDS	86506650	86507566	.	-	0	Parent=g31624.t1

This does not look right (duplicate exons, overlapping CDSs), and it causes gffread to crash when attempting to extract protein sequences. I ran the following command:

lifton \
    -g $GFF \
    -o sample.lifton.gff3 \
    -copies \
    --threads 10 \
    $TARGET \
    $REF

using LiftOn v1.0.5. Unfortunately I can't currently share my input data.