Need some critical insights:) (any help is highly appreciated)

Hi:( I am doing my MSc dissertation in Plant Molecular Biology and Biotechnology and my topic of research is the role of tetraspanins in abiotic stresses. Long story short i have crossed two singles mutants in arabidopsis (tet2 and tet3) to generate double mutant tet2/3 for confirm functional redundancy . I performed tdna screening for double mutant and obtained one line where i have only gotten bands with tdna insertion and not genomic bands in the double mutant. However when the said homozygous double mutant line was taken for qrtpcr showed a fold change of 0.5 and 0.8 for tet 2 in tet2/3 mutant across two independent biological replicates . What is the possible reason for that? Is my plant heterozygous (never gotten genomic band for tet2 in tet2/3 mutant) . One interesting point is that cis nat is formed which overlaps with exon1 of TET2 gene and tdna insertion is in the second exon. Does the cis nat that is produced somewhere stabilizing the truncated transcript and slight expression seen in qrtpcr . I am running out of ideas .

Any help would be highly appreciated:)