The Sample IDs in your metadata are not 100% matching your Sample IDs in your Feature Table provided as input to core-metrics-phylogenetic. Can you share your feature-table summarize results? You will almost certainly need to run the command sans metadata.
Sorry for my late answer, I figured out that I make a mistake on my sample ID on my metadata.
In the computer of the MiSeq I labeled my samples as “01,02,03…”. The problem was when I opened the metadata generated by the machine in Libre Office because my sample “01” appeared as “1” and so on. So when I run the command it appeared as if they were samples missing. I had to modify my metadata by writing the sample ID’s as text in order to be able to write “01” in Libre Office. In that way qiime was able to detect my samples and perform correctly the analysis!