so only what is left is ledger bug
Not really.
The most probable case (as already mentioned by multiple people here) is that YOU have done a mistake.
An extremely rare ledger bug which only happened to one person doesn't sound realistic at all..
Sometimes it is hard to accept.. but 98% of
computer problems are caused by the person in front of it.
Next time, make sure you backup the correct seed, reinitialize it and test whether it reproduces the correct addresses. Only then store funds there.