Creating an instance in OWLready2 creates a completely new class instead of asigning it to the existing class

I'm trying to create a simple ontology, following the tutorial on the official website. The code runs smoothly and everything seems fine when running this code:

import owlready2
owlready2.JAVA_EXE = r"my-path-to-java-exe"          

# new.owl is a non-existing file and therefore onto has no pre-defined classes
# if you know of any nicer way to define an ontology, I'd appreciate it

onto = get_ontology("new.owl")

with onto:
    class Drug(Thing): pass
    class number_of_tablets(Drug >> int, FunctionalProperty): pass          # Creating some properties
    class price(Drug >> float, FunctionalProperty): pass
    class price_per_tablet(Drug >> float, FunctionalProperty): pass

    rule = Imp()

    # Rule: "Drug instance ?d     AND     price of ?d is ?p     AND     drug ?d has number_of_tablets = ?n
    #        AND     ?r = ?p/?n     ->      Drug ?d has price_per_tablet = ?r"
    
    rule.set_as_rule("""Drug(?d), price(?d,?p), number_of_tablets(?d,?n), divide(?r, ?p, ?n) -> price_per_tablet(?d, ?r)""")

    # Create an instance "drug" with properties defined in brackets
    drug = Drug(number_of_tablets = 10, price = 25.0)
    #print(drug.iri)

    # Syncing the reasoner infers new info
    sync_reasoner_pellet(infer_property_values = True, infer_data_property_values = True)

    # New property price_per_tablet is now added to drug and we can use it normally:
    print(drug.price_per_tablet)

# Save this ontology with rules in the same folder, filename: test
onto.save(file = "test", format = "rdfxml")

Problem: When I open the resulting file "test" in Protégé, my instance "drug1" is not a part of the previously defined class Drug but of a new class of the same name Drug (I'll always denote this one in italic so it doesn't get confusing). Interestingly, this new class Drug is not even a subclass of owl:Thing class.

I'm not sure what's the problem. According to Protégé, the defined class Drug has IRI: file:/C:/.../new#Drug, and the other class Drug has IRI: new#Drug.

When I checked IRIs of all the described objects in Python, they were all synchronized.

I'm very confused about what happened here.

I checked the "test" file and the part concerning this instance is:

<Drug rdf:about="#drug1">
  <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
  <number_of_tablets rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">10</number_of_tablets>
  <price rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">25.0</price>
  <price_per_tablet rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.5</price_per_tablet>
</Drug>

This is confusing because when I opened the file PizzaTutorial.owl from the famous Pizza tutorial, an instance was defined like this:

<owl:NamedIndividual rdf:about="http://www.semanticweb.org/pizzatutorial/ontologies/2020/PizzaTutorial#AmericanaHotPizza2">
        <rdf:type rdf:resource="http://www.semanticweb.org/pizzatutorial/ontologies/2020/PizzaTutorial#AmericanaHotPizza"/>
        <hasCaloricContent rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">675</hasCaloricContent>
    </owl:NamedIndividual>

What happened?!

Another question: When I inspected the individual in Protégé, I noticed that the properties number_of_tablets and price were added as Annotations, and not as Data Properties. I assume that this is the reason why my SWRL rule (which was correctly exported) doesn't conclude the price_per_tablet property for this individual when I remove the sync_reasoner line.

Please comment on anything you notice is wrong, I'm a beginner in ontology programming and in both tools and I would very much appreciate your help!