Сам спросил - сам ответил.
Вот что на это отвечает саппорт ботов телеграмма:
It is because you are not sending the "offset" parameter, you need to do it, otherwise we will continue sending you the first 100 updates.
getUpdates return first 100 unconfirmed updates.
To confirm an update, use offset while requesting getUpdates.
All updates less than or equal to offset are maked as confirmed and deleted from server.
