anyone can help to understand what is the cause of the rot?
It looks like Botrytis cinerea (aka grey mould) or similar. This sometimes infects young capsicum fruit but can then become dormant until they start to ripen. It only takes one infected fruit in a greenhouse to produce millions of spores which can infect other fruit and flowers so your best bet is to regularly inspect and remove anything which looks as if it is infected. Commercial growers can probably use preventative fungicides not available to the public. Fungal infections often start in areas which have gotten wet, so if growing under cover then make sure to only water the plants at the roots and avoid wetting leaves, flowers or fruit.