Hello Diego,
If the default fallback is activated then maybe the intent (just before the checkpoint) is not recognised. You can check that if you run with the debug flag rasa shell --debug. Another reason that fallback is activated is when it fails to predict the next action (as also described in this post). Btw, more info on the fallback you can find in the docs here.
Also, I just thought that another way to double check that the problem is not on checkpoints is to remove them temporarily and create independent stories. Then if you see that the bot is working as expected without checkpoints then yes the problem is how you implement them. However, if you still have the same errors then the problem is elsewhere.
Sharing your pipeline from config.yml might also help.