The following CDS isoforms have one or more exons that overlap with an exon of another isoform of the same gene, but they are not in the same frame/phase.
Are both of these overlapping exons real?
F44F1.6b
K02E7.1b
T16A1.1a
Y75B8A.9b
K10B3.6a
B0302.1c
Y67H2A.2b
C10C6.7b
They all appear to be based on rather dubious EST or OST alignments except for Y67H2A.2band C10C6.7b.
They do not have orthologs in the overlapped region.
The only ones that I am at all comfortable with are T16A1.1b which has lots of paralogs and Y67H2A.2b and C10C6.7b which I made 
Regards,
Gary