Although at least in my field the problem is that no one ever thought to set lower limits on the quality of what you can call a genome. So now we get "genomes" made up of 100,000 contigs (many only a couple of hundred base pairs long) and even counting all of those, the total sequence might account for only 70% of the total size of the genome. But it's still a "genome" paper, which is still an instant ticket to Nature Genetics (or Nature Biotechnology if the assembly is REALLY bad).
BGI is certainly one of the biggest offenders (Cucumber and Pigeonpea are both examples of the sort of terrible genomes-in-name-only BGI puts out) but I think the real problem is that Illumina sequence data is so cheap people keep trying to use it to sequence genomes, thinking if they throw enough raw data and enough mate-pair libraries at the problem it'll eventually make up for the fact that Illumina reads are so short. Illumina data is great for a lot of things. Calling SNPs, measuring gene expression, studying methylation patterns.
But, at least for any genome significant transposon content, it simply does not work.