Hi @Liviacmg,
Welcome to the messy world of taxonomy! 
There is not necessarily a problem with the different classifiers per se. However, the various reference databases often follow different nomenclatural rules, and implement different taxonomic schemas. This is often confounded by the increasing pace in which microbial taxonomy is changing and being updated. It is quite difficult for the groups that curate these different databases to keep up. Especially, with the decline of formally trained taxonomists these days. 
There are also taxonomic inconsistencies within various taxonomic groups of a single database too. See this example from our RESCRIPt tutorial.
Again, it has more to do with how often the databases are updated and curated rather than capabilities of a classification algorithm. It is the old "garbage in garbage out". Your classification is as only as good as your reference database. 
This is why we even provide tools like RESCRIPt, to help users better curate their reference databases. Especially if they know more about the taxonomy of the groups they are interested in, e.g. fix an incorrect reference taxonomy.
Sadly there is no simple fix to this...
In addition to the Kraken and SILVA databases I'd also suggest using Greengenes2.