Yesterday I had a nice talk with the guys from python-telegram-bot package about what is happening, and they help me to solve it using the Telegram Bot API.
Basically it seems that Rasa Telegram connector is not handling the Updates properly, and there were some messages which did not receive something call the offset (I think is a reply saying that the message was received maybe) the offset should be set with a number equal to update_id+1. Then what I did was:
Stop Rasa instance
Delete Webhook (Telegram Bot API)
Update offset value(update_id)(Telegram Bot API)
start rasa again
I think something should be solve on the side of the Telegram connector in this function