Hello @Gabriel_Pires!
Great question. I have a couple of suggestions but I don't know if it is the answer. The problem is that you table includes sequences that are not in your phylogeny.
It looks like you already made sure that you are not filtering out sequences but I would first make sure that you are not discarding too many samples with your sampling depth. Mike Robson does a great job explaining why here: The table does not appear to be completely represented by the phylogeny.
My next suggestion would be to make sure the names are the same in your rooted tree ID's and your table ID's. Matt gives a great explanation in this post with a similar problem. feature ids much be present as tip names in phylogeny
I hope that helps. Let me know if it doesn't and we will brainstorm some more!
Chloe 