Hello @Gabriel_Pires,
I am sorry for the slow response on my part.
This seems perfectly reasonable and is more than likely not the cause of the issue! 
There isn't another file to check, however, I am pretty sure that the issue lies in your feature IDs and not your sample IDs. So you might have checked the wrong column. I recommend following Matt's steps here again but checking the feature IDs.
If that does not work could you post your code and results(for Matt's steps) so that I have a better idea of what is happening. Also if you want to post your rooted tree and table that you are using I could also try to debug more effectively. :qiime2:
I hope this helps!
Chloe 